To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("recount")

In most cases, you don't need to download the package archive at all.

recount

 

   

Explore and download data from the recount project

Bioconductor version: Release (3.4)

Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://biorxiv.org/content/early/2016/08/08/068478.

Author: Leonardo Collado-Torres [aut, cre], Abhinav Nellore [ctb], Andrew E. Jaffe [ctb], Margaret A. Taub [ctb], Kai Kammers [ctb], Shannon E. Ellis [ctb], Kasper Daniel Hansen [ctb], Ben Langmead [ctb], Jeffrey T. Leek [aut, ths]

Maintainer: Leonardo Collado-Torres <lcollado at jhu.edu>

Citation (from within R, enter citation("recount")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("recount")

Documentation

HTML R Script Basic DESeq2 results exploration
HTML R Script recount quick start guide
PDF   Reference Manual
Text   NEWS

Details

biocViews Coverage, DataImport, DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software
Version 1.0.12
In Bioconductor since BioC 3.4 (R-3.3) (< 6 months)
License Artistic-2.0
Depends R (>= 3.3.0), SummarizedExperiment
Imports BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb, GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer(>= 1.33.11), S4Vectors, stats, utils
LinkingTo
Suggests AnnotationDbi, BiocStyle, DESeq2, devtools (>= 1.6), EnsDb.Hsapiens.v79, GenomicFeatures, knitcitations, knitr (>= 1.6), org.Hs.eg.db, regionReport, rmarkdown (>= 0.9.5), testthat
SystemRequirements
Enhances
URL https://github.com/leekgroup/recount
BugReports https://github.com/leekgroup/recount/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source recount_1.0.12.tar.gz
Windows Binary recount_1.0.12.zip
Mac OS X 10.9 (Mavericks) recount_1.0.12.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/recount/tree/release-3.4
Package Short Url http://bioconductor.org/packages/recount/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: