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() setting value
version R version 3.3.1 (2016-06-21)
system x86_64, darwin13.4.0
ui X11
language (EN)
collate en_CA.UTF-8
tz America/Vancouver
date 2016-12-03
package * version date source
acepack 1.4.1 2016-10-29 CRAN (R 3.3.0)
annotate 1.52.0 2016-10-18 Bioconductor
AnnotationDbi 1.36.0 2016-10-18 Bioconductor
assertthat 0.1 2013-12-06 CRAN (R 3.3.0)
backports 1.0.4 2016-10-24 CRAN (R 3.3.0)
Biobase 2.34.0 2016-10-18 Bioconductor
BiocGenerics 0.20.0 2016-10-18 Bioconductor
BiocParallel 1.8.1 2016-10-30 Bioconductor
biomaRt 2.30.0 2016-10-18 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.3.0)
car 2.1-3 2016-08-11 CRAN (R 3.3.0)
caret * 6.0-73 2016-11-10 CRAN (R 3.3.2)
class 7.3-14 2015-08-30 CRAN (R 3.3.1)
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 1.3-1 2016-11-18 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 1.9.8 2016-11-25 CRAN (R 3.3.2)
DBI 0.5-1 2016-09-10 CRAN (R 3.3.0)
DESeq2 1.14.0 2016-10-18 Bioconductor
devtools 1.12.0 2016-06-24 CRAN (R 3.3.0)
digest 0.6.10 2016-08-02 CRAN (R 3.3.0)
doMC 1.3.4 2015-10-13 CRAN (R 3.3.0)
dplyr 0.5.0 2016-06-24 CRAN (R 3.3.0)
e1071 1.6-7 2015-08-05 CRAN (R 3.3.0)
evaluate 0.10 2016-10-11 CRAN (R 3.3.0)
forcats 0.1.1 2016-09-16 CRAN (R 3.3.0)
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 1.56.0 2016-10-18 Bioconductor
geneplotter 1.52.0 2016-10-18 Bioconductor
GenomeInfoDb 1.10.1 2016-11-04 Bioconductor
GenomicRanges 1.26.1 2016-10-20 Bioconductor
ggplot2 * 2.2.0 2016-11-11 CRAN (R 3.3.2)
ggrepel 0.6.5 2016-11-24 CRAN (R 3.3.2)
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 4.0-0 2016-11-01 CRAN (R 3.3.0)
htmlTable 1.7 2016-10-19 CRAN (R 3.3.0)
htmltools 0.3.5 2016-03-21 CRAN (R 3.3.0)
IRanges 2.8.1 2016-11-08 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 3.3.1)
Matrix 1.2-7.1 2016-09-01 CRAN (R 3.3.0)
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 1.8-16 2016-11-07 CRAN (R 3.3.0)
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 3.1-128 2016-05-10 CRAN (R 3.3.1)
nloptr 1.0.4 2014-08-04 CRAN (R 3.3.0)
nnet 7.3-12 2016-02-02 CRAN (R 3.3.1)
pbkrtest 0.4-6 2016-01-27 CRAN (R 3.3.0)
pheatmap 1.0.8 2015-12-11 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 0.12.8 2016-11-17 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)
reshape2 1.4.2 2016-10-22 CRAN (R 3.3.0)
rmarkdown 1.2 2016-11-21 CRAN (R 3.3.2)
rpart 4.1-10 2015-06-29 CRAN (R 3.3.1)
rprojroot 1.1 2016-10-29 CRAN (R 3.3.0)
RSQLite 1.1 2016-11-27 CRAN (R 3.3.0)
rstudioapi 0.6 2016-06-27 CRAN (R 3.3.0)
S4Vectors 0.12.0 2016-10-18 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 1.4.0 2016-10-18 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 0.6.0 2016-08-12 CRAN (R 3.3.0)
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 0.14.0 2016-10-18 Bioconductor
yaml 2.1.14 2016-11-12 CRAN (R 3.3.2)
zlibbioc 1.20.0 2016-10-18 Bioconductor