sessionInfo()
## R version 3.3.1 (2016-06-21)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 14.04.4 LTS
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
## [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 methods stats graphics utils datasets grDevices base
##
## other attached packages:
## [1] systemPipeR_1.6.2 ShortRead_1.30.0 GenomicAlignments_1.8.3
## [4] SummarizedExperiment_1.2.3 Biobase_2.32.0 BiocParallel_1.6.2
## [7] Rsamtools_1.24.0 Biostrings_2.40.2 XVector_0.12.0
## [10] GenomicRanges_1.24.2 GenomeInfoDb_1.8.1 IRanges_2.6.1
## [13] S4Vectors_0.10.1 BiocGenerics_0.18.0 BiocStyle_2.0.2
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.5 lattice_0.20-33 GO.db_3.3.0 digest_0.6.9
## [5] plyr_1.8.4 BatchJobs_1.6 backports_1.0.2 RSQLite_1.0.0
## [9] evaluate_0.9 ggplot2_2.1.0 zlibbioc_1.18.0 GenomicFeatures_1.24.3
## [13] annotate_1.50.0 Matrix_1.2-6 checkmate_1.8.0 rmarkdown_0.9.6
## [17] GOstats_2.38.0 splines_3.3.1 stringr_1.0.0 pheatmap_1.0.8
## [21] RCurl_1.95-4.8 biomaRt_2.28.0 munsell_0.4.3 sendmailR_1.2-1
## [25] rtracklayer_1.32.1 base64enc_0.1-3 BBmisc_1.9 htmltools_0.3.5
## [29] fail_1.3 edgeR_3.14.0 codetools_0.2-14 XML_3.98-1.4
## [33] AnnotationForge_1.14.2 bitops_1.0-6 grid_3.3.1 RBGL_1.48.1
## [37] xtable_1.8-2 GSEABase_1.34.0 gtable_0.2.0 DBI_0.4-1
## [41] magrittr_1.5 formatR_1.4 scales_0.4.0 graph_1.50.0
## [45] stringi_1.1.1 hwriter_1.3.2 genefilter_1.54.2 limma_3.28.10
## [49] latticeExtra_0.6-28 brew_1.0-6 rjson_0.2.15 RColorBrewer_1.1-2
## [53] tools_3.3.1 Category_2.38.0 survival_2.39-4 yaml_2.1.13
## [57] AnnotationDbi_1.34.3 colorspace_1.2-6 knitr_1.13