Contents

The ExperimentHub server provides easy R / Bioconductor access to large files of data.

1 ExperimentHub objects

The ExperimentHub package provides a client interface to resources stored at the ExperimentHub web service. It has similar functionality to AnnotationHub package.

library(ExperimentHub)

The ExperimentHub package is straightforward to use. Create an ExperiemntHub object

eh = ExperimentHub()
## snapshotDate(): 2018-04-27

Now at this point you have already done everything you need in order to start retrieving experiment data. For most operations, using the ExperimentHub object should feel a lot like working with a familiar list or data.frame and has all of the functionality of an Hub object like AnnotationHub package’s AnnotationHub object.

Lets take a minute to look at the show method for the hub object eh

eh
## ExperimentHub with 1211 records
## # snapshotDate(): 2018-04-27 
## # $dataprovider: Eli and Edythe L. Broad Institute of Harvard and MIT, NA...
## # $species: Homo Sapiens, Homo sapien, Homo sapiens, Mus musculus, Mus Mu...
## # $rdataclass: ExpressionSet, SummarizedExperiment, RaggedExperiment, Dat...
## # additional mcols(): taxonomyid, genome, description,
## #   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
## #   tags, rdatapath, sourceurl, sourcetype 
## # retrieve records with, e.g., 'object[["EH1"]]' 
## 
##            title                                                           
##   EH1    | RNA-Sequencing and clinical data for 7706 tumor samples from ...
##   EH166  | ERR188297                                                       
##   EH167  | ERR188088                                                       
##   EH168  | ERR188204                                                       
##   EH169  | ERR188317                                                       
##   ...      ...                                                             
##   EH1403 | leukocyte.betas                                                 
##   EH1404 | ref.methylation                                                 
##   EH1405 | age.inference                                                   
##   EH1406 | ethnicity.inference                                             
##   EH1407 | sex.inference

You can see that it gives you an idea about the different types of data that are present inside the hub. You can see where the data is coming from (dataprovider), as well as what species have samples present (species), what kinds of R data objects could be returned (rdataclass). We can take a closer look at all the kinds of data providers that are available by simply looking at the contents of dataprovider as if it were the column of a data.frame object like this:

unique(eh$dataprovider)
##  [1] "GEO"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
##  [2] "GEUVADIS"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
##  [3] "Allen Brain Atlas"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
##  [4] "ArrayExpress"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
##  [5] "Department of Psychology, Abdul Haq Campus, Federal Urdu University for Arts, Science and Technology, Karachi, Pakistan. shahiq_psy@yahoo.com"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
##  [6] "Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
##  [7] "INRA, Institut National de la Recherche Agronomique, US1367 Metagenopolis, 78350 Jouy en Josas, France."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
##  [8] "Institute of Microbiology and Infection, University of Birmingham, Birmingham, England."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
##  [9] "1] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark. [2] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark. [3]."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
## [10] "1] Department of Anthropology, University of Oklahoma, Dale Hall Tower, 521 Norman, Oklahoma 73019, USA [2] Universidad Científica del Sur, Lima 18, Perú [3] City of Hope, NCI-designated Comprehensive Cancer Center, Duarte, California 91010, USA."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
## [11] "Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
## [12] "BGI-Shenzhen, Shenzhen 518083, China."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
## [13] "1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [3]."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
## [14] "Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
## [15] "NA"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
## [16] "Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
## [17] "Centre for Integrative Biology, University of Trento, Trento, Italy."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
## [18] "Computational Biology Institute, George Washington University , Ashburn, VA , USA ; Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Facultad de Ciencias Biologicas , Santiago , Chile."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
## [19] "Genome Institute of Singapore, Singapore 138672, Singapore."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
## [20] "[1] BGI-Shenzhen, Shenzhen 518083, China [2] Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
## [21] "Luxembourg Centre for Systems Biomedicine, 7 avenue des Hauts-Fourneaux, 4362 Esch-sur-Alzette, Luxembourg."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
## [22] "Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
## [23] "[1] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark. [2] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark. [3]."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
## [24] "[1] Department of Anthropology, University of Oklahoma, Dale Hall Tower, 521 Norman, Oklahoma 73019, USA [2] Universidad Cientifica del Sur, Lima 18, Peru [3] City of Hope, NCI-designated Comprehensive Cancer Center, Duarte, California 91010, USA."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
## [25] "Centre de Recherche en Infectiologie, CHU de Quebec-Universite Laval, Quebec, Canada."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
## [26] "Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
## [27] "Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
## [28] "BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
## [29] "Department of Medicine & Therapeutics, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
## [30] "[1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [3]."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
## [31] "1000 Genomes Project"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
## [32] "yriMulti"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
## [33] "10x Genomics"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
## [34] "Illumina 450 methylation assay"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
## [35] "GTex"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
## [36] "Eli and Edythe L. Broad Institute of Harvard and MIT"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
## [37] "Harmonized Cancer Datasets Genomic Data Commons Data Portal"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
## [38] "[1] 1] BGI-Shenzhen, Shenzhen, China. [2] BGI Hong Kong Research Institute, Hong Kong, China. [3] School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China. [4]., [2] 1] BGI-Shenzhen, Shenzhen, China. [2]., [3] 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3]., [4] European Molecular Biology Laboratory, Heidelberg, Germany., [5] 1] BGI-Shenzhen, Shenzhen, China. [2] European Molecular Biology Laboratory, Heidelberg, Germany. [3] The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark., [6] INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France., [7] The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark., [8] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark., [9] Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, Barcelona, Spain., [10] BGI-Shenzhen, Shenzhen, China., [11] 1] Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia. [2] Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, KAU, Jeddah, Saudi Arabia., [12] 1] Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, KAU, Jeddah, Saudi Arabia. [2] Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia., [13] 1] BGI-Shenzhen, Shenzhen, China. [2] Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, KAU, Jeddah, Saudi Arabia. [3] James D. Watson Institute of Genome Science, Hangzhou, China., [14] 1] BGI-Shenzhen, Shenzhen, China. [2] James D. Watson Institute of Genome Science, Hangzhou, China., [15] Department of Biology, University of Copenhagen, Copenhagen, Denmark., [16] NA, [17] 1] INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France. [2] Centre for Host-Microbiome Interactions, Dental Institute Central Office, King's College London, Guy's Hospital, London Bridge, UK., [18] NA, [19] 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3] The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. [4] Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, KAU, Jeddah, Saudi Arabia. [5] Macau University of Science and Technology, Macau, China."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
## [39] "NIH Common Fund Human Microbiome Project"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
## [40] "10X Genomics"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
## [41] "Array Express"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
## [42] "PubMed"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
## [43] "GDC"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
## [44] "European Molecular Biology Laboratory"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
## [45] "DKFZ"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
## [46] "MDAnderson"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
## [47] "EGA"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
## [48] "paper supplementary"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
## [49] "SMD"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
## [50] "TCGA"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
## [51] "ICGC"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
## [52] "Private"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
## [53] "[1] Centre for Integrative Biology, University of Trento, Trento, Italy., [2] Azienda Provinciale per i Servizi Sanitari, Trento, Italy."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
## [54] "[1] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA., [2] Broad Institute of MIT and Harvard, Cambridge, MA., [3] Sandia National Laboratories, Livermore, CA., [4] Wildlife Conservation Society, Suva, Fiji., [5] Edith Cowan University, Western Australia., [6] University of Helsinki, Helsinki, Finland., [7] Massachusetts General Hospital, Boston, MA., [8] Center for Microbiome, Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
## [55] "[1] Computational Biology Institute, George Washington University , Ashburn, VA , USA ; Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Facultad de Ciencias Biologicas , Santiago , Chile., [2] Computational Biology Institute, George Washington University , Ashburn, VA , USA., [3] Computational Biology Institute, George Washington University , Ashburn, VA , USA ; CIBIO-InBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos, Universidade do Porto , Vairao , USA ; Division of Emergency Medicine, Children's National Medical Center , Washington, D.C. , USA., [4] Stanley Neurovirology Laboratory, Johns Hopkins School of Medicine , Baltimore, MD , USA., [5] Sheppard Pratt Hospital , Baltimore, MD , USA., [6] Schroeder Statistical Consulting LLC , Ellicott City, MD , USA."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
## [56] "[1] Genome Institute of Singapore, Singapore 138672, Singapore., [2] Institute of Medical Biology, Singapore 138648, Singapore., [3] Institute of Molecular and Cell Biology, Singapore 138673, Singapore., [4] Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China., [5] Institute of Biomedical Studies, Baylor University, Waco, Texas 76798, USA., [6] Department of Biological Sciences, National University of Singapore, Singapore 117543., [7] Singapore Immunology Network, Singapore 138648, Singapore., [8] Division of Plastic, Reconstructive &Aesthetic Surgery, National University Health System, Singapore 119074, Singapore., [9] National Skin Centre, Singapore 308205, Singapore., [10] Department of Microbiology and Immunology, National University of Singapore, Singapore 117545, Singapore."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
## [57] "[1] 1] BGI-Shenzhen, Shenzhen 518083, China [2] Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark., [2] 1] BGI-Shenzhen, Shenzhen 518083, China [2] School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China., [3] BGI-Shenzhen, Shenzhen 518083, China., [4] Department of Internal Medicine, Hospital Oberndorf, Teaching Hospital of the Paracelsus Private University of Salzburg, Paracelsusstrasse 37, 5110 Oberndorf, Austria., [5] 1] BGI-Shenzhen, Shenzhen 518083, China [2] School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China [3] BGI Hong Kong Research Institute, Hong Kong, China., [6] 1] BGI-Shenzhen, Shenzhen 518083, China [2] Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia., [7] 1] BGI-Shenzhen, Shenzhen 518083, China [2] The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark., [8] First Department of Internal Medicine, Medical University Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria., [9] 1] BGI-Shenzhen, Shenzhen 518083, China [2] Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark [3] Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia [4] Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
## [58] "[1] Luxembourg Centre for Systems Biomedicine, 7 avenue des Hauts-Fourneaux, 4362 Esch-sur-Alzette, Luxembourg., [2] Integrated BioBank of Luxembourg, 6 rue Nicolas Ernest Barble, 1210 Luxembourg, Luxembourg., [3] Department of Internal Medicine II, Saarland University Medical Center, 66421 Homburg, Germany., [4] Centre Hospitalier Emile Mayrisch, Rue Emile Mayrisch, 4240 Esch-sur-Alzette, Luxembourg., [5] Clinique Pediatrique - Centre Hospitalier de Luxembourg, 4 rue Nicolas Ernest Barble, 1210 Luxembourg."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
## [59] "[1] Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
## [60] "[1] INRA, Institut National de la Recherche Agronomique, US1367 Metagenopolis, 78350 Jouy en Josas, France."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
## [61] "[1] 1] BGI-Shenzhen, Shenzhen, China. [2] BGI Hong Kong Research Institute, Hong Kong, China. [3] School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China. [4]., [2] 1] BGI-Shenzhen, Shenzhen, China. [2]., [3] 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3]., [4] European Molecular Biology Laboratory, Heidelberg, Germany., [5] 1] BGI-Shenzhen, Shenzhen, China. [2] European Molecular Biology Laboratory, Heidelberg, Germany. [3] The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark., [6] INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France., [7] The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark., [8] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark., [9] Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, Barcelona, Spain., [10] BGI-Shenzhen, Shenzhen, China., [11] 1] Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia. [2] Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, KAU, Jeddah, Saudi Arabia., [12] 1] Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, KAU, Jeddah, Saudi Arabia. [2] Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia., [13] 1] BGI-Shenzhen, Shenzhen, China. [2] Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, KAU, Jeddah, Saudi Arabia. [3] James D. Watson Institute of Genome Science, Hangzhou, China., [14] 1] BGI-Shenzhen, Shenzhen, China. [2] James D. Watson Institute of Genome Science, Hangzhou, China., [15] Department of Biology, University of Copenhagen, Copenhagen, Denmark., [16] 1] INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France. [2] INRA, Institut National de la Recherche Agronomique, Unite mixte de Recherche 14121 Microbiologie de l'Alimentation au Service de la Sante, Jouy en Josas, France., [17] 1] INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France. [2] Centre for Host-Microbiome Interactions, Dental Institute Central Office, King's College London, Guy's Hospital, London Bridge, UK., [18] 1] European Molecular Biology Laboratory, Heidelberg, Germany. [2] Max Delbruck Centre for Molecular Medicine, Berlin, Germany., [19] 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3] The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. [4] Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, KAU, Jeddah, Saudi Arabia. [5] Macau University of Science and Technology, Macau, China."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
## [62] "[1] Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Disease of China, National Center for Cardiovascular Diseases of China, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China., [2] Department of Cardiology, Beijing ChaoYang Hospital, Capital Medical University, Beijing, 100020, China., [3] Beijing Key Laboratory of Hypertension, Beijing, 100020, China., [4] Computational Genomics Laboratory, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China., [5] Novogene Bioinformatics Institute, Beijing, 100000, China., [6] Department of Cardiology, Baoding NO.1 Central Hospital, Baoding, 071000, China., [7] Department of Cardiology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, 710061, China., [8] Department of Cardiology Kailuan General Hospital, Hebei Union University, Tangshan, 063000, China., [9] Department of Biomedical Informatics, Centre for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, 100191, China., [10] Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA., [11] Medical Research Center, Beijing ChaoYang Hospital, Capital Medical University, Beijing, 100020, China., [12] Department of Stem Cell Engineering, Texas Heart Institute, Houston, TX, 77030, USA., [13] Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China., [14] Department of Cardiology, Beijing ChaoYang Hospital, Capital Medical University, Beijing, 100020, China. yxc6229@sina.com., [15] Beijing Key Laboratory of Hypertension, Beijing, 100020, China. yxc6229@sina.com., [16] CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. zhubaoli@im.ac.cn., [17] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China. zhubaoli@im.ac.cn., [18] Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Disease of China, National Center for Cardiovascular Diseases of China, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China. caijun@fuwaihospital.org."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
## [63] "[1] Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China., [2] RealBio Genomic Institute, Shanghai 200050, China., [3] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University, Hangzhou 310003, China."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
## [64] "[1] Institute of Microbiology and Infection, University of Birmingham, Birmingham, England."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
## [65] "[1] Institute of Clinical Nutrition, University of Hohenheim, Stuttgart, Germany., [2] Algorithms in Bioinformatics, University of Tubingen, Tubingen, Germany."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
## [66] "[1] 1] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark. [2] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark. [3]., [2] 1] INRA, Institut National de la Recherche Agronomique, UMR 14121 MICALIS, Jouy en Josas, France. [2] INRA, Institut National de la Recherche Agronomique, US 1367 Metagenopolis, Jouy en Josas, France. [3] Department of Computer Science, Center for Bioinformatics and Computational Biology, University of Maryland, USA. [4]., [3] 1] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark. [2] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark., [4] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark., [5] 1] BGI Hong Kong Research Institute, Hong Kong, China. [2] BGI-Shenzhen, Shenzhen, China. [3] School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China., [6] European Molecular Biology Laboratory, Heidelberg, Germany., [7] 1] INRA, Institut National de la Recherche Agronomique, UMR 14121 MICALIS, Jouy en Josas, France. [2] INRA, Institut National de la Recherche Agronomique, US 1367 Metagenopolis, Jouy en Josas, France., [8] 1] Commissariat a l'Energie Atomique et aux Energies Alternatives, Institut de Genomique, Evry, France. [2] Centre National de la Recherche Scientifique, Evry, France. [3] Universite d'Evry Val d'Essonne, Evry, France., [9] The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark., [10] Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, Barcelona, Spain., [11] 1] BGI-Shenzhen, Shenzhen, China. [2] European Molecular Biology Laboratory, Heidelberg, Germany. [3] The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark., [12] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark., [13] 1] The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark. [2] Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark., [14] 1] Department of Structural Biology, VIB, Brussels, Belgium. [2] Department of Bioscience Engineering, Vrije Universiteit, Brussels, Belgium., [15] National Food Institute, Division for Epidemiology and Microbial Genomics, Technical University of Denmark, Kongens Lyngby, Denmark., [16] 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark., [17] 1] The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark. [2] Hagedorn Research Institute, Gentofte, Denmark. [3] Institute of Biomedical Science, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. [4] Faculty of Health, Aarhus University, Aarhus, Denmark., [18] 1] BGI Hong Kong Research Institute, Hong Kong, China. [2] BGI-Shenzhen, Shenzhen, China., [19] 1] Department of Bioscience Engineering, Vrije Universiteit, Brussels, Belgium. [2] Department of Microbiology and Immunology, Rega Institute, KU Leuven, Belgium. [3] VIB Center for the Biology of Disease, Leuven, Belgium., [20] Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark., [21] Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands., [22] 1] European Molecular Biology Laboratory, Heidelberg, Germany. [2] Department of Biological Information, Tokyo Institute of Technology, Yokohama, Japan., [23] INRA, Institut National de la Recherche Agronomique, UMR 14121 MICALIS, Jouy en Josas, France., [24] 1] European Molecular Biology Laboratory, Heidelberg, Germany. [2] Max Delbruck Centre for Molecular Medicine, Berlin, Germany., [25] 1] BGI-Shenzhen, Shenzhen, China. [2] The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark. [3] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [4] Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia., [26] 1] INRA, Institut National de la Recherche Agronomique, UMR 14121 MICALIS, Jouy en Josas, France. [2] INRA, Institut National de la Recherche Agronomique, US 1367 Metagenopolis, Jouy en Josas, France. [3] King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, United Kingdom."
## [67] "[1] 1] Department of Anthropology, University of Oklahoma, Dale Hall Tower, 521 Norman, Oklahoma 73019, USA [2] Universidad Cientifica del Sur, Lima 18, Peru [3] City of Hope, NCI-designated Comprehensive Cancer Center, Duarte, California 91010, USA., [2] 1] Department of Anthropology, University of Oklahoma, Dale Hall Tower, 521 Norman, Oklahoma 73019, USA [2] Universidad Cientifica del Sur, Lima 18, Peru, [3] City of Hope, NCI-designated Comprehensive Cancer Center, Duarte, California 91010, USA., [4] Department of Anthropology, University of Oklahoma, Dale Hall Tower, 521 Norman, Oklahoma 73019, USA., [5] Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA., [6] Departments of Pediatrics and Computer Science &Engineering University of California San Diego, La Jolla, CA 92093, USA., [7] Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, USA., [8] Instituto Nacional de Salud, Lima 11, Peru, [9] Old Dominion University, Norfolk, Virginia 23529, USA., [10] Universidad Cientifica del Sur, Lima 18, Peru"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
## [68] "[1] Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA., [2] 1] Dermatology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA [2]., [3] 1] Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA [2]."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
## [69] "[1] BGI-Shenzhen, Shenzhen 518083, China."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
## [70] "[1] 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [3]., [2] 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2]., [3] 1] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2]., [4] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China., [5] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France., [6] 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China., [7] 1] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2] King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, London SE1 9RT, UK., [8] 1] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [2] Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University, 310003 Hangzhou, China."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
## [71] "[1] Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy., [2] Plant Foods in Hominin Dietary Ecology Research Group, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany. Electronic address: stephanie_schnorr@eva.mpg.de., [3] Institute of Biomedical Technologies, Italian National Research Council, Segrate, Milan 20090, Italy., [4] Metabolism, Anthropometry, and Nutrition Laboratory, Department of Anthropology, University of Nevada, Las Vegas, NV 89154-5003, USA., [5] Plant Foods in Hominin Dietary Ecology Research Group, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany., [6] Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy. Electronic address: marco.candela@unibo.it."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
## [72] "[1] Centre de Recherche en Infectiologie, CHU de Quebec-Universite Laval, Quebec, Canada., [2] Institut National de Sante Publique du Quebec, Laboratoire de Sante Publique du Quebec, Montreal, Quebec, Canada."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
## [73] "[1] Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA., [2] Human Food Project, 53600 Highway 118, Terlingua, TX 79852, USA., [3] The Department of Twin Research and Genetic Epidemiology, King's College London, St. Thomas' Hospital, Lambeth Palace Road, London SE1 7EH, UK., [4] Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94025, USA., [5] Lawson Health Research Institute and Western University, London, Ontario N6A 4V2, Canada., [6] Departments of Pediatrics and Computer Science and Engineering and Center for Microbiome Innovation, University of California, San Diego, CA 92093, USA., [7] National Institute for Medical Research, Mwanza 11101, Tanzania., [8] School of Medicine and Department of Anthropology, New York University, New York, NY, USA."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
## [74] "[1] Centre for Integrative Biology, University of Trento, Trento, Italy., [2] Istituto G.B. Mattei, Comano, Italy., [3] NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, Trento, Italy., [4] Department of Medicine, Section of Dermatology, University of Verona, Verona, Italy."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
## [75] "[1] Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada., [2] Genome Quebec Innovation Centre, McGill University, Montreal, Quebec, Canada., [3] Jewish General Hospital, Montreal, Quebec, Canada., [4] Devil's Staircase Consulting, North Vancouver, British Columbia, Canada., [5] New York Genome Center, New York, NY, USA., [6] Department of Human Genetics, McGill University, Montreal, Quebec, Canada., [7] School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada. amee.manges@ubc.ca."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
## [76] "[1] Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America., [2] Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States of America., [3] Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany., [4] Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany., [5] Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany., [6] Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany., [7] Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany., [8] Max Delbruck Centre for Molecular Medicine, Berlin, Germany., [9] Department of Bioinformatics Biocenter, University of Wurzburg, Wurzburg, Germany."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
## [77] "[1] BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China., [2] BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China; Macau University of Science and Technology, Taipa, Macau 999078, China., [3] BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China., [4] BGI-Shenzhen, Shenzhen 518083, China., [5] Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK., [6] BGI-Shenzhen, Shenzhen 518083, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China., [7] BGI-Shenzhen, Shenzhen 518083, China; Qingdao University-BGI Joint Innovation College, Qingdao University, Qingdao 266071, China., [8] BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China., [9] BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China., [10] BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China., [11] BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark., [12] BGI-Shenzhen, Shenzhen 518083, China; Macau University of Science and Technology, Taipa, Macau 999078, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China., [13] BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China. Electronic address: lijunhua@genomics.cn., [14] Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK. Electronic address: tim.spector@kcl.ac.uk., [15] BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Macau University of Science and Technology, Taipa, Macau 999078, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China. Electronic address: jiahuijue@genomics.cn."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
## [78] "[1] Department of Medicine & Therapeutics, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong., [2] BGI-Shenzhen, Shenzhen, China., [3] Department of Biology, University of Copenhagen, Copenhagen, Denmark., [4] Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark., [5] Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia., [6] Department of Surgical Gastroenterology, Hvidovre Hospital, Hvidovre, Denmark., [7] National Institute of Nutrition and Seafood Research, Bergen, Norway., [8] Department of Internal Medicine, Hospital Oberndorf, Q3 Teaching Hospital of the Paracelsus Private University of Salzburg, Oberndorf, Austria., [9] First Department of Internal Medicine, Medical University Innsbruck, Innsbruck, Austria., [10] The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark., [11] Macau University of Science and Technology, Macau, China."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
## [79] "[1] Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany., [2] Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Universite Paris-Est Creteil, Creteil, France., [3] Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Department of Applied Tumor Biology, Institute of Pathology University Hospital Heidelberg, Heidelberg, Germany Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany., [4] Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Universite Paris-Est Creteil, Creteil, France., [5] Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany., [6] Department of Surgery, APHP and UPEC Universite Paris-Est Creteil, Creteil, France., [7] Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany., [8] Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany., [9] Department of Radiology, APHP and UPEC Universite Paris-Est Creteil, Creteil, France., [10] Department of Medical Oncology, APHP and UPEC Universite Paris-Est Creteil, Creteil, France., [11] Department of Pathology and LIC-EA4393-EC2M3, APHP and UPEC Universite Paris-Est Creteil, Creteil, France., [12] Department of Biological Information, Tokyo Institute of Technology, Tokyo, Japan., [13] Department of Applied Tumor Biology, Institute of Pathology University Hospital Heidelberg, Heidelberg, Germany Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany., [14] Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, USA., [15] Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Universite Paris-Est Creteil, Creteil, France iradj.sobhani@hmn.aphp.fr bork@embl.de., [16] Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany Max Delbruck Centre for Molecular Medicine, Berlin, Germany iradj.sobhani@hmn.aphp.fr bork@embl.de."                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
## [80] "GRCh"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
## [81] "Illumina Inc"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
## [82] "Wanding Zhou <zhouwanding@gmail.com>"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
## [83] "Steve Horvath"

In the same way, you can also see data from different species inside the hub by looking at the contents of species like this:

head(unique(eh$species))
## [1] "Homo sapiens"            "Mus musculus"           
## [3] "Homo Sapiens"            "Mus musculus (E18 mice)"
## [5] "Mus Musculus (E18 mice)" "Mus Musculus"

And this will also work for any of the other types of metadata present. You can learn which kinds of metadata are available by simply hitting the tab key after you type ‘eh$’. In this way you can explore for yourself what kinds of data are present in the hub right from the command line. This interface also allows you to access the hub programatically to extract data that matches a particular set of criteria.

Another valuable types of metadata to pay attention to is the rdataclass.

head(unique(eh$rdataclass))
## [1] "ExpressionSet"              "GAlignmentPairs"           
## [3] "CellMapperList"             "gds.class"                 
## [5] "RangedSummarizedExperiment" "GRanges"

The rdataclass allows you to see which kinds of R objects the hub will return to you. This kind of information is valuable both as a means to filter results and also as a means to explore and learn about some of the kinds of experimenthub objects that are widely available for the project. Right now this is a pretty short list, but over time it should grow as we support more of the different kinds of experimenthub objects via the hub.

Now lets try getting the data files associated with the r Biocpkg("alpineData") package using the query method. The query method lets you search rows for specific strings, returning an ExperimentHub instance with just the rows matching the query. The preparerclass column of metadata monitors which package is associated with the ExperimentHub data.

One can get chain files for Drosophila melanogaster from UCSC with:

apData <- query(eh, "alpineData")
apData
## ExperimentHub with 4 records
## # snapshotDate(): 2018-04-27 
## # $dataprovider: GEUVADIS
## # $species: Homo sapiens
## # $rdataclass: GAlignmentPairs
## # additional mcols(): taxonomyid, genome, description,
## #   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
## #   tags, rdatapath, sourceurl, sourcetype 
## # retrieve records with, e.g., 'object[["EH166"]]' 
## 
##           title    
##   EH166 | ERR188297
##   EH167 | ERR188088
##   EH168 | ERR188204
##   EH169 | ERR188317

Query has worked and you can now see that the only data present is provided by the “alpineData”.

The metadata underlying this hub object can be retrieved by you

apData$preparerclass
## [1] "alpineData" "alpineData" "alpineData" "alpineData"
df <- mcols(apData)

By default the show method will only display the first 5 and last 5 rows. There are hundreds of records present in the hub.

length(eh)
## [1] 1211

Lets look at another example, where we pull down only data from the hub for species “mus musculus”.

mm <- query(eh, "mus musculus")
mm
## ExperimentHub with 13 records
## # snapshotDate(): 2018-04-27 
## # $dataprovider: 10X Genomics, DKFZ, 10x Genomics, ArrayExpress, GEO
## # $species: Mus musculus, Mus Musculus (E18 mice), Mus Musculus, Mus musc...
## # $rdataclass: character, RangedSummarizedExperiment, SummarizedExperimen...
## # additional mcols(): taxonomyid, genome, description,
## #   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
## #   tags, rdatapath, sourceurl, sourcetype 
## # retrieve records with, e.g., 'object[["EH173"]]' 
## 
##            title                                                           
##   EH173  | Pre-processed microarray data from the Affymetrix MG-U74Av2 p...
##   EH552  | st100k                                                          
##   EH553  | st400k                                                          
##   EH554  | full_1Mneurons                                                  
##   EH557  | tasicST6                                                        
##   ...      ...                                                             
##   EH1042 | Brain scRNA-seq data, gene (row) annotation                     
##   EH1072 | Bisulfite sequencing data from tissue Tregs (per sample)        
##   EH1073 | Bisulfite sequencing data from tissue Tregs (per tissue/cell ...
##   EH1074 | RNA-seq data from tissue Tregs (RPKM values)                    
##   EH1075 | RNA-seq data from tissue Tregs (htseq values)

We can also look at the ExperimentHub object in a browser using the display() function. We can then filter the ExperimentHub object using the Global search field on the top right corner of the page or the in-column search fields.

d <- display(eh)

2 Using ExperimentHub to retrieve data

Looking back at our alpineData file example, if we are interested in the first file, we can gets its metadata using

apData
## ExperimentHub with 4 records
## # snapshotDate(): 2018-04-27 
## # $dataprovider: GEUVADIS
## # $species: Homo sapiens
## # $rdataclass: GAlignmentPairs
## # additional mcols(): taxonomyid, genome, description,
## #   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
## #   tags, rdatapath, sourceurl, sourcetype 
## # retrieve records with, e.g., 'object[["EH166"]]' 
## 
##           title    
##   EH166 | ERR188297
##   EH167 | ERR188088
##   EH168 | ERR188204
##   EH169 | ERR188317
apData["EH166"]
## ExperimentHub with 1 record
## # snapshotDate(): 2018-04-27 
## # names(): EH166
## # package(): alpineData
## # $dataprovider: GEUVADIS
## # $species: Homo sapiens
## # $rdataclass: GAlignmentPairs
## # $rdatadateadded: 2016-07-21
## # $title: ERR188297
## # $description: Subset of aligned reads from sample ERR188297
## # $taxonomyid: 9606
## # $genome: GRCh38
## # $sourcetype: FASTQ
## # $sourceurl: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188297/ERR1882...
## # $sourcesize: NA
## # $tags: c("Sequencing", "RNASeq", "GeneExpression",
## #   "Transcription") 
## # retrieve record with 'object[["EH166"]]'

We can download the file using

apData[["EH166"]]
## see ?alpineData and browseVignettes('alpineData') for documentation
## downloading 0 resources
## loading from cache 
##     '/home/biocbuild//.ExperimentHub/166'
## Loading required package: GenomicAlignments
## Loading required package: S4Vectors
## Loading required package: stats4
## 
## Attaching package: 'S4Vectors'
## The following object is masked from 'package:base':
## 
##     expand.grid
## Loading required package: IRanges
## Loading required package: GenomeInfoDb
## Loading required package: GenomicRanges
## Loading required package: SummarizedExperiment
## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## 
## Attaching package: 'Biobase'
## The following object is masked from 'package:ExperimentHub':
## 
##     cache
## The following object is masked from 'package:AnnotationHub':
## 
##     cache
## Loading required package: DelayedArray
## Loading required package: matrixStats
## 
## Attaching package: 'matrixStats'
## The following objects are masked from 'package:Biobase':
## 
##     anyMissing, rowMedians
## Loading required package: BiocParallel
## 
## Attaching package: 'DelayedArray'
## The following objects are masked from 'package:matrixStats':
## 
##     colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
## The following objects are masked from 'package:base':
## 
##     aperm, apply
## Loading required package: Biostrings
## Loading required package: XVector
## 
## Attaching package: 'Biostrings'
## The following object is masked from 'package:DelayedArray':
## 
##     type
## The following object is masked from 'package:base':
## 
##     strsplit
## Loading required package: Rsamtools
## GAlignmentPairs object with 25531 pairs, strandMode=1, and 0 metadata columns:
##           seqnames strand   :              ranges  --              ranges
##              <Rle>  <Rle>   :           <IRanges>  --           <IRanges>
##       [1]        1      +   : 108560389-108560463  -- 108560454-108560528
##       [2]        1      -   : 108560454-108560528  -- 108560383-108560457
##       [3]        1      +   : 108560534-108600608  -- 108600626-108606236
##       [4]        1      -   : 108569920-108569994  -- 108569825-108569899
##       [5]        1      -   : 108587954-108588028  -- 108587881-108587955
##       ...      ...    ... ...                 ... ...                 ...
##   [25527]        X      +   : 119790596-119790670  -- 119790717-119790791
##   [25528]        X      +   : 119790988-119791062  -- 119791086-119791160
##   [25529]        X      +   : 119791037-119791111  -- 119791142-119791216
##   [25530]        X      +   : 119791348-119791422  -- 119791475-119791549
##   [25531]        X      +   : 119791376-119791450  -- 119791481-119791555
##   -------
##   seqinfo: 194 sequences from an unspecified genome

Each file is retrieved from the ExperimentHub server and the file is also cache locally, so that the next time you need to retrieve it, it should download much more quickly.

3 Configuring ExperimentHub objects

When you create the ExperimentHub object, it will set up the object for you with some default settings. See ?ExperimentHub for ways to customize the hub source, the local cache, and other instance-specific options, and ?getExperimentHubOption to get or set package-global options for use across sessions.

If you look at the object you will see some helpful information about it such as where the data is cached and where online the hub server is set to.

eh
## ExperimentHub with 1211 records
## # snapshotDate(): 2018-04-27 
## # $dataprovider: Eli and Edythe L. Broad Institute of Harvard and MIT, NA...
## # $species: Homo Sapiens, Homo sapien, Homo sapiens, Mus musculus, Mus Mu...
## # $rdataclass: ExpressionSet, SummarizedExperiment, RaggedExperiment, Dat...
## # additional mcols(): taxonomyid, genome, description,
## #   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
## #   tags, rdatapath, sourceurl, sourcetype 
## # retrieve records with, e.g., 'object[["EH1"]]' 
## 
##            title                                                           
##   EH1    | RNA-Sequencing and clinical data for 7706 tumor samples from ...
##   EH166  | ERR188297                                                       
##   EH167  | ERR188088                                                       
##   EH168  | ERR188204                                                       
##   EH169  | ERR188317                                                       
##   ...      ...                                                             
##   EH1403 | leukocyte.betas                                                 
##   EH1404 | ref.methylation                                                 
##   EH1405 | age.inference                                                   
##   EH1406 | ethnicity.inference                                             
##   EH1407 | sex.inference

By default the ExperimentHub object is set to the latest snapshotData and a snapshot version that matches the version of Bioconductor that you are using. You can also learn about these data with the appropriate methods.

snapshotDate(eh)
## [1] "2018-04-27"

If you are interested in using an older version of a snapshot, you can list previous versions with the possibleDates() like this:

pd <- possibleDates(eh)
pd
##  [1] "2016-02-23" "2016-06-07" "2016-07-14" "2016-07-21" "2016-08-08"
##  [6] "2016-10-01" "2017-06-09" "2017-08-25" "2017-10-06" "2017-10-10"
## [11] "2017-10-12" "2017-10-16" "2017-10-19" "2017-10-26" "2017-10-30"
## [16] "2017-10-29" "2018-01-08" "2018-02-02" "2018-02-09" "2018-02-22"
## [21] "2018-03-16" "2018-03-30" "2018-04-02" "2018-04-10" "2018-04-20"
## [26] "2018-04-25" "2018-04-26" "2018-04-27" "2018-04-27"

Set the dates like this:

snapshotDate(ah) <- pd[1]

4 ExperimentHub

5 Session info

sessionInfo()
## R version 3.5.0 (2018-04-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.4 LTS
## 
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.7-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.7-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] GenomicAlignments_1.16.0    Rsamtools_1.32.0           
##  [3] Biostrings_2.48.0           XVector_0.20.0             
##  [5] SummarizedExperiment_1.10.0 DelayedArray_0.6.0         
##  [7] BiocParallel_1.14.0         matrixStats_0.53.1         
##  [9] Biobase_2.40.0              GenomicRanges_1.32.0       
## [11] GenomeInfoDb_1.16.0         IRanges_2.14.0             
## [13] S4Vectors_0.18.0            alpineData_1.5.0           
## [15] ExperimentHub_1.6.0         AnnotationHub_2.12.0       
## [17] BiocGenerics_0.26.0         BiocStyle_2.8.0            
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.16                  compiler_3.5.0               
##  [3] BiocInstaller_1.30.0          later_0.7.1                  
##  [5] zlibbioc_1.26.0               bitops_1.0-6                 
##  [7] tools_3.5.0                   digest_0.6.15                
##  [9] bit_1.1-12                    lattice_0.20-35              
## [11] RSQLite_2.1.0                 evaluate_0.10.1              
## [13] memoise_1.1.0                 pkgconfig_2.0.1              
## [15] Matrix_1.2-14                 shiny_1.0.5                  
## [17] DBI_0.8                       curl_3.2                     
## [19] yaml_2.1.18                   xfun_0.1                     
## [21] GenomeInfoDbData_1.1.0        httr_1.3.1                   
## [23] stringr_1.3.0                 knitr_1.20                   
## [25] grid_3.5.0                    rprojroot_1.3-2              
## [27] bit64_0.9-7                   R6_2.2.2                     
## [29] AnnotationDbi_1.42.0          rmarkdown_1.9                
## [31] bookdown_0.7                  blob_1.1.1                   
## [33] magrittr_1.5                  backports_1.1.2              
## [35] promises_1.0.1                htmltools_0.3.6              
## [37] mime_0.5                      interactiveDisplayBase_1.18.0
## [39] xtable_1.8-2                  httpuv_1.4.1                 
## [41] stringi_1.1.7                 RCurl_1.95-4.10