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 3.3.0 (2016-05-03)
system x86_64, darwin13.4.0
ui X11
language (EN)
collate en_CA.UTF-8
tz America/Vancouver
date 2016-11-09
package * version date source
acepack 1.4.0 2016-10-20 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)
Biobase 2.32.0 2016-05-04 Bioconductor
BiocGenerics 0.18.0 2016-05-04 Bioconductor
BiocParallel 1.6.6 2016-08-15 Bioconductor
biomaRt 2.28.0 2016-05-05 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 * 6.0-71 2016-08-05 CRAN (R 3.3.0)
chron 2.3-47 2015-06-24 CRAN (R 3.3.0)
class 7.3-14 2015-08-30 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 1.2-7 2016-10-11 CRAN (R 3.3.0)
cowplot 0.6.3 2016-09-30 CRAN (R 3.3.0)
crayon 1.3.2 2016-06-28 CRAN (R 3.3.0)
data.table 1.9.6 2015-09-19 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 0.6.10 2016-08-02 cran (@0.6.10)
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 (@1.4.3)
foreign 0.8-67 2016-09-13 CRAN (R 3.3.0)
formatR 1.4 2016-05-09 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 * 2.1.0 2016-03-01 CRAN (R 3.3.0)
ggrepel 0.6.3 2016-10-20 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 3.17-4 2016-05-02 CRAN (R 3.3.0)
htmltools 0.3.5 2016-03-21 CRAN (R 3.3.0)
IRanges 2.6.1 2016-06-19 Bioconductor
iterators 1.0.8 2015-10-13 cran (@1.0.8)
knitr 1.14 2016-08-13 CRAN (R 3.3.0)
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 1.2-7.1 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 1.8-15 2016-09-14 CRAN (R 3.3.0)
minqa 1.2.4 2014-10-09 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 3.3.0)
nloptr 1.0.4 2014-08-04 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)
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 0.12.7 2016-09-05 cran (@0.12.7)
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 1.1 2016-10-16 CRAN (R 3.3.0)
rpart 4.1-10 2015-06-29 CRAN (R 3.3.0)
RSQLite 1.0.0 2014-10-25 CRAN (R 3.3.0)
S4Vectors 0.10.3 2016-08-16 Bioconductor
scales 0.4.0.9003 2016-10-24 Github (hadley/scales@d58d83a)
SparseM 1.72 2016-09-06 CRAN (R 3.3.0)
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 2.39-5 2016-06-26 CRAN (R 3.3.0)
testthat 1.0.2 2016-04-23 CRAN (R 3.3.0)
tibble 1.2 2016-08-26 cran (@1.2)
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 3.98-1.4 2016-03-01 CRAN (R 3.3.0)
xtable 1.8-2 2016-02-05 CRAN (R 3.3.0)
XVector 0.12.1 2016-07-22 Bioconductor
yaml 2.1.13 2014-06-12 CRAN (R 3.3.0)
zlibbioc 1.18.0 2016-05-04 Bioconductor