diffloop: Identifying differential DNA loops from chromatin topology data

Caleb Lareau & Martin Aryee

2017-10-30

library(diffloop)
library(diffloopdata)
library(ggplot2)
library(GenomicRanges)
library(ggrepel)
library(DESeq2)

About

Due to the maintainer’s inability to figure out data package resubmission to Bioc, a compiled vignette is hosted here.

Notes on Data

All data used in these analyses were processed from GEO and are contained in the diffloopdata package. Please feel free to contact Caleb (the maintainer) with any questions concerning the data or this workflow. The diffloopdata package is available here

Session info

sessionInfo()
## R Under development (unstable) (2017-10-20 r73567)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.3 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] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] DESeq2_1.19.0              SummarizedExperiment_1.9.0
##  [3] DelayedArray_0.5.0         matrixStats_0.52.2        
##  [5] Biobase_2.39.0             ggrepel_0.7.0             
##  [7] GenomicRanges_1.31.0       GenomeInfoDb_1.15.0       
##  [9] IRanges_2.13.0             S4Vectors_0.17.0          
## [11] BiocGenerics_0.25.0        ggplot2_2.2.1             
## [13] diffloopdata_1.5.0         diffloop_1.7.0            
## 
## loaded via a namespace (and not attached):
##  [1] bitops_1.0-6             bit64_0.9-7             
##  [3] RColorBrewer_1.1-2       progress_1.1.2          
##  [5] rprojroot_1.2            tools_3.5.0             
##  [7] backports_1.1.1          R6_2.2.2                
##  [9] rpart_4.1-11             Hmisc_4.0-3             
## [11] DBI_0.7                  lazyeval_0.2.1          
## [13] colorspace_1.3-2         nnet_7.3-12             
## [15] gridExtra_2.3            prettyunits_1.0.2       
## [17] bit_1.1-12               compiler_3.5.0          
## [19] htmlTable_1.9            rtracklayer_1.39.0      
## [21] scales_0.5.0             checkmate_1.8.5         
## [23] readr_1.1.1              genefilter_1.61.0       
## [25] pbapply_1.3-3            stringr_1.2.0           
## [27] digest_0.6.12            Rsamtools_1.31.0        
## [29] foreign_0.8-69           rmarkdown_1.6           
## [31] XVector_0.19.0           base64enc_0.1-3         
## [33] pkgconfig_2.0.1          htmltools_0.3.6         
## [35] limma_3.35.0             htmlwidgets_0.9         
## [37] rlang_0.1.2              RSQLite_2.0             
## [39] bindr_0.1                zoo_1.8-0               
## [41] BiocParallel_1.13.0      acepack_1.4.1           
## [43] dplyr_0.7.4              RCurl_1.95-4.8          
## [45] magrittr_1.5             Sushi_1.17.0            
## [47] GenomeInfoDbData_0.99.1  Formula_1.2-2           
## [49] Matrix_1.2-11            Rcpp_0.12.13            
## [51] munsell_0.4.3            stringi_1.1.5           
## [53] yaml_2.1.14              edgeR_3.21.0            
## [55] zlibbioc_1.25.0          plyr_1.8.4              
## [57] grid_3.5.0               blob_1.1.0              
## [59] lattice_0.20-35          Biostrings_2.47.0       
## [61] splines_3.5.0            annotate_1.57.0         
## [63] hms_0.3                  locfit_1.5-9.1          
## [65] knitr_1.17               geneplotter_1.57.0      
## [67] reshape2_1.4.2           codetools_0.2-15        
## [69] biomaRt_2.35.0           XML_3.98-1.9            
## [71] glue_1.2.0               evaluate_0.10.1         
## [73] latticeExtra_0.6-28      data.table_1.10.4-3     
## [75] foreach_1.4.3            gtable_0.2.0            
## [77] assertthat_0.2.0         xtable_1.8-2            
## [79] survival_2.41-3          tibble_1.3.4            
## [81] iterators_1.0.8          GenomicAlignments_1.15.0
## [83] AnnotationDbi_1.41.0     memoise_1.1.0           
## [85] bindrcpp_0.2             cluster_2.0.6           
## [87] statmod_1.4.30

Citations

\(^1\)Hnisz, Denes, et al. “Activation of proto-oncogenes by disruption of chromosome neighborhoods.” Science (2016).

\(^2\)Ji, Xiong, et al. “3D Chromosome Regulatory Landscape of Human Pluripotent Cells.” Cell stem cell (2015).

\(^3\)Phanstiel, D, et al. “Mango: A bias correcting ChIA-PET analysis pipeline.” Bioinformatics (2015).

\(^4\)Robinson, M, et al. “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics (2010).

\(^5\)Law, C, et al. “Voom: precision weights unlock linear model analysis tools for RNA-seq read counts.” Genome Biology (2014).