For the sake of reproducibility, here’s a list of packages and their versions that were used to create this R markdown document.
devtools::session_info()## Session info --------------------------------------------------------------## setting value
## version R version 3.3.0 (2016-05-03)
## system x86_64, darwin13.4.0
## ui RStudio (1.0.136)
## language (EN)
## collate en_CA.UTF-8
## tz America/Vancouver
## date 2017-02-18## Packages ------------------------------------------------------------------## package * version date source
## acepack 1.4.1 2016-10-29 CRAN (R 3.3.0)
## annotate 1.50.1 2016-10-09 Bioconductor
## AnnotationDbi 1.34.4 2016-07-08 Bioconductor
## assertthat 0.1 2013-12-06 CRAN (R 3.3.0)
## backports 1.0.5 2017-01-18 CRAN (R 3.3.2)
## base64enc 0.1-3 2015-07-28 CRAN (R 3.3.0)
## Biobase * 2.32.0 2016-05-04 Bioconductor
## BiocGenerics * 0.18.0 2016-05-04 Bioconductor
## BiocParallel 1.6.6 2016-08-15 Bioconductor
## bitops 1.0-6 2013-08-17 CRAN (R 3.3.0)
## car 2.1-4 2016-12-02 CRAN (R 3.3.2)
## caret * 6.0-73 2016-11-10 CRAN (R 3.3.2)
## checkmate 1.8.2 2016-11-02 CRAN (R 3.3.0)
## cluster * 2.0.5 2016-10-08 CRAN (R 3.3.0)
## codetools 0.2-15 2016-10-05 CRAN (R 3.3.0)
## colorspace 1.3-2 2016-12-14 CRAN (R 3.3.2)
## cowplot 0.7.0 2016-10-28 CRAN (R 3.3.0)
## crayon 1.3.2 2016-06-28 CRAN (R 3.3.0)
## data.table 1.10.4 2017-02-01 CRAN (R 3.3.0)
## DBI 0.5-1 2016-09-10 CRAN (R 3.3.0)
## DESeq2 1.12.4 2016-08-08 Bioconductor
## devtools 1.12.0 2016-06-24 CRAN (R 3.3.0)
## digest 0.6.12 2017-01-27 CRAN (R 3.3.2)
## doMC * 1.3.4 2015-10-13 CRAN (R 3.3.0)
## doParallel * 1.0.10 2015-10-14 CRAN (R 3.3.0)
## dplyr 0.5.0 2016-06-24 CRAN (R 3.3.0)
## evaluate 0.10 2016-10-11 CRAN (R 3.3.0)
## forcats 0.2.0 2017-01-23 CRAN (R 3.3.2)
## foreach * 1.4.3 2015-10-13 CRAN (R 3.3.0)
## foreign 0.8-67 2016-09-13 CRAN (R 3.3.0)
## Formula 1.2-1 2015-04-07 CRAN (R 3.3.0)
## genefilter 1.54.2 2016-05-16 Bioconductor
## geneplotter 1.50.0 2016-05-04 Bioconductor
## GenomeInfoDb 1.8.7 2016-09-02 Bioconductor
## GenomicRanges 1.24.3 2016-09-11 Bioconductor
## ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.3.2)
## ggrepel 0.6.5 2016-11-24 CRAN (R 3.3.2)
## gridBase 0.4-7 2014-02-24 CRAN (R 3.3.0)
## gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.0)
## gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
## highr 0.6 2016-05-09 CRAN (R 3.3.0)
## Hmisc 4.0-2 2016-12-31 CRAN (R 3.3.2)
## htmlTable 1.9 2017-01-26 CRAN (R 3.3.2)
## htmltools 0.3.5 2016-03-21 CRAN (R 3.3.0)
## htmlwidgets 0.8 2016-11-09 CRAN (R 3.3.2)
## IRanges 2.6.1 2016-06-19 Bioconductor
## iterators * 1.0.8 2015-10-13 CRAN (R 3.3.0)
## knitr 1.15.1 2016-11-22 CRAN (R 3.3.2)
## labeling 0.3 2014-08-23 CRAN (R 3.3.0)
## lattice * 0.20-34 2016-09-06 CRAN (R 3.3.0)
## latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.0)
## lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.0)
## lme4 1.1-12 2016-04-16 CRAN (R 3.3.0)
## locfit 1.5-9.1 2013-04-20 CRAN (R 3.3.0)
## magrittr * 1.5 2014-11-22 CRAN (R 3.3.0)
## MASS 7.3-45 2016-04-21 CRAN (R 3.3.0)
## Matrix 1.2-8 2017-01-20 CRAN (R 3.3.2)
## MatrixModels 0.4-1 2015-08-22 CRAN (R 3.3.0)
## matrixStats 0.51.0 2016-10-09 CRAN (R 3.3.0)
## memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
## mgcv 1.8-17 2017-02-08 CRAN (R 3.3.2)
## minqa 1.2.4 2014-10-09 CRAN (R 3.3.0)
## ModelMetrics 1.1.0 2016-08-26 CRAN (R 3.3.0)
## munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
## nlme 3.1-131 2017-02-06 CRAN (R 3.3.2)
## nloptr 1.0.4 2014-08-04 CRAN (R 3.3.0)
## NMF * 0.20.6 2015-05-26 CRAN (R 3.3.0)
## nnet 7.3-12 2016-02-02 CRAN (R 3.3.0)
## pbkrtest 0.4-6 2016-01-27 CRAN (R 3.3.0)
## pheatmap 1.0.8 2015-12-11 CRAN (R 3.3.0)
## pkgmaker * 0.22 2014-05-14 CRAN (R 3.3.0)
## plyr 1.8.4 2016-06-08 CRAN (R 3.3.0)
## purrr 0.2.2 2016-06-18 CRAN (R 3.3.0)
## quantreg 5.29 2016-09-04 CRAN (R 3.3.0)
## R6 2.2.0 2016-10-05 CRAN (R 3.3.0)
## randomForest * 4.6-12 2015-10-07 CRAN (R 3.3.0)
## RColorBrewer * 1.1-2 2014-12-07 CRAN (R 3.3.0)
## Rcpp 0.12.9 2017-01-14 CRAN (R 3.3.2)
## RCurl 1.95-4.8 2016-03-01 CRAN (R 3.3.0)
## readr 1.0.0 2016-08-03 CRAN (R 3.3.0)
## registry * 0.3 2015-07-08 CRAN (R 3.3.0)
## reshape2 1.4.2 2016-10-22 CRAN (R 3.3.0)
## rmarkdown 1.3 2016-12-21 CRAN (R 3.3.0)
## rngtools * 1.2.4 2014-03-06 CRAN (R 3.3.0)
## rpart 4.1-10 2015-06-29 CRAN (R 3.3.0)
## rprojroot 1.2 2017-01-16 CRAN (R 3.3.2)
## RSQLite 1.1-2 2017-01-08 CRAN (R 3.3.2)
## S4Vectors 0.10.3 2016-08-16 Bioconductor
## scales 0.4.1 2016-11-09 CRAN (R 3.3.2)
## SparseM 1.74 2016-11-10 CRAN (R 3.3.2)
## stringi 1.1.2 2016-10-01 CRAN (R 3.3.0)
## stringr 1.1.0 2016-08-19 CRAN (R 3.3.0)
## SummarizedExperiment 1.2.3 2016-06-10 Bioconductor
## survival 2.40-1 2016-10-30 CRAN (R 3.3.0)
## testthat 1.0.2 2016-04-23 CRAN (R 3.3.0)
## tibble 1.2 2016-08-26 CRAN (R 3.3.0)
## tidyr 0.6.1 2017-01-10 CRAN (R 3.3.2)
## withr 1.0.2 2016-06-20 CRAN (R 3.3.0)
## XML 3.98-1.5 2016-11-10 CRAN (R 3.3.2)
## xtable 1.8-2 2016-02-05 CRAN (R 3.3.0)
## XVector 0.12.1 2016-07-22 Bioconductor
## yaml 2.1.14 2016-11-12 CRAN (R 3.3.2)
## zlibbioc 1.18.0 2016-05-04 Bioconductor