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 3.3.2 (2016-10-31)
system x86_64, darwin13.4.0
ui RStudio (1.0.136)
language (EN)
collate en_CA.UTF-8
tz America/Vancouver
date 2017-03-27
package * version date source
acepack 1.4.1 2016-10-29 CRAN (R 3.3.0)
affy 1.52.0 2016-10-18 Bioconductor
affyio 1.44.0 2016-10-18 Bioconductor
annotate 1.52.1 2016-12-22 Bioconductor
AnnotationDbi 1.36.2 2017-01-30 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 * 2.34.0 2016-10-18 Bioconductor
BiocGenerics * 0.20.0 2016-10-18 Bioconductor
BiocInstaller 1.24.0 2016-10-18 Bioconductor
BiocParallel 1.8.1 2016-10-30 Bioconductor
biomaRt * 2.30.0 2016-10-18 Bioconductor
Biostrings 2.42.1 2016-12-01 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.3.0)
broom 0.4.2 2017-02-13 CRAN (R 3.3.2)
BSgenome 1.42.0 2016-10-18 Bioconductor
BSgenome.Hsapiens.UCSC.hg38 1.4.1 2017-03-08 Bioconductor
changepoint 2.2.2 2016-10-04 CRAN (R 3.3.0)
checkmate 1.8.2 2016-11-02 CRAN (R 3.3.0)
circlize 0.3.10 2017-03-07 CRAN (R 3.3.2)
class 7.3-14 2015-08-30 CRAN (R 3.3.2)
cluster * 2.0.5 2016-10-08 CRAN (R 3.3.2)
codetools 0.2-15 2016-10-05 CRAN (R 3.3.2)
colorspace 1.3-2 2016-12-14 CRAN (R 3.3.2)
cometExactTest 0.1.3 2015-10-31 CRAN (R 3.3.0)
ComplexHeatmap 1.12.0 2016-10-14 Bioconductor (R 3.3.1)
corrplot 0.77 2016-04-21 CRAN (R 3.3.0)
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 0.6 2017-03-09 CRAN (R 3.3.2)
dendextend 1.4.0 2017-01-21 cran (@1.4.0)
DEoptimR 1.0-8 2016-11-19 cran (@1.0-8)
DESeq2 * 1.14.1 2016-12-01 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)
diptest 0.75-7 2015-06-08 cran (@0.75-7)
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)
DPpackage 1.1-6 2012-09-14 CRAN (R 3.3.0)
evaluate 0.10 2016-10-11 CRAN (R 3.3.0)
FField 0.1.0 2013-06-28 CRAN (R 3.3.0)
flexmix 2.3-13 2015-01-17 cran (@2.3-13)
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 3.3.2)
Formula 1.2-1 2015-04-07 CRAN (R 3.3.0)
fpc 2.1-10 2015-08-14 cran (@2.1-10)
genefilter 1.56.0 2016-10-18 Bioconductor
geneplotter 1.52.0 2016-10-18 Bioconductor
GenomeInfoDb * 1.10.3 2017-02-07 Bioconductor
GenomicAlignments 1.10.0 2016-10-18 Bioconductor
GenomicFeatures 1.26.3 2017-02-22 Bioconductor
GenomicRanges * 1.26.3 2017-02-25 Bioconductor
GenVisR 1.4.7 2017-03-09 Github (griffithlab/GenVisR@974177f)
GetoptLong 0.1.6 2017-03-07 CRAN (R 3.3.2)
ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.3.2)
ggrepel 0.6.5 2016-11-24 CRAN (R 3.3.2)
GlobalOptions 0.0.11 2017-03-06 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)
gtools 3.5.0 2015-05-29 CRAN (R 3.3.0)
haven 1.0.0 2016-09-23 CRAN (R 3.3.0)
hexbin * 1.27.1 2015-08-19 CRAN (R 3.3.0)
Hmisc 4.0-2 2016-12-31 CRAN (R 3.3.2)
hms 0.3 2016-11-22 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)
httr 1.2.1 2016-07-03 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)
jsonlite 1.3 2017-02-28 CRAN (R 3.3.2)
kernlab 0.9-25 2016-10-03 cran (@0.9-25)
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 3.3.2)
latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.0)
lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.0)
limma 3.30.12 2017-03-05 Bioconductor
locfit 1.5-9.1 2013-04-20 CRAN (R 3.3.0)
lubridate 1.6.0 2016-09-13 CRAN (R 3.3.0)
maftools * 1.0.50 2017-02-23 Bioconductor
magrittr * 1.5 2014-11-22 CRAN (R 3.3.0)
MASS 7.3-45 2016-04-21 CRAN (R 3.3.2)
Matrix 1.2-8 2017-01-20 CRAN (R 3.3.2)
matrixStats * 0.51.0 2016-10-09 CRAN (R 3.3.0)
mclust 5.2.2 2017-01-22 cran (@5.2.2)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
mgcv 1.8-17 2017-02-08 CRAN (R 3.3.2)
mnormt 1.5-5 2016-10-15 CRAN (R 3.3.0)
modelr 0.1.0 2016-08-31 CRAN (R 3.3.0)
modeltools 0.2-21 2013-09-02 cran (@0.2-21)
munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
mvtnorm 1.0-6 2017-03-02 CRAN (R 3.3.2)
nlme 3.1-131 2017-02-06 CRAN (R 3.3.2)
NMF * 0.20.6 2015-05-26 CRAN (R 3.3.0)
nnet 7.3-12 2016-02-02 CRAN (R 3.3.2)
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)
prabclus 2.2-6 2015-01-14 cran (@2.2-6)
preprocessCore 1.36.0 2016-10-18 Bioconductor
psych 1.6.12 2017-01-08 CRAN (R 3.3.2)
purrr * 0.2.2 2016-06-18 CRAN (R 3.3.0)
R6 2.2.0 2016-10-05 CRAN (R 3.3.0)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.3.0)
Rcpp 0.12.10 2017-03-19 cran (@0.12.10)
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)
readxl 0.1.1.9000 2017-02-22 Github (tidyverse/readxl@3338f92)
registry * 0.3 2015-07-08 CRAN (R 3.3.0)
reshape2 1.4.2 2016-10-22 CRAN (R 3.3.0)
rjson 0.2.15 2014-11-03 CRAN (R 3.3.0)
rmarkdown * 1.3 2016-12-21 CRAN (R 3.3.2)
rngtools * 1.2.4 2014-03-06 CRAN (R 3.3.0)
robustbase 0.92-7 2016-12-09 cran (@0.92-7)
rpart 4.1-10 2015-06-29 CRAN (R 3.3.2)
rprojroot 1.2 2017-01-16 CRAN (R 3.3.2)
Rsamtools 1.26.1 2016-10-22 Bioconductor
RSQLite 1.1-2 2017-01-08 CRAN (R 3.3.2)
rtracklayer 1.34.2 2017-02-19 Bioconductor
rvest 0.3.2 2016-06-17 CRAN (R 3.3.0)
S4Vectors * 0.12.1 2016-12-01 Bioconductor
scales 0.4.1 2016-11-09 CRAN (R 3.3.2)
shape 1.4.2 2014-11-05 CRAN (R 3.3.0)
slam 0.1-40 2016-12-01 CRAN (R 3.3.2)
stringi 1.1.2 2016-10-01 CRAN (R 3.3.0)
stringr 1.2.0 2017-02-18 CRAN (R 3.3.2)
SummarizedExperiment * 1.4.0 2016-10-18 Bioconductor
survival 2.40-1 2016-10-30 CRAN (R 3.3.0)
sva 3.22.0 2016-10-18 Bioconductor
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)
tidyverse * 1.1.1 2017-01-27 CRAN (R 3.3.2)
trimcluster 0.1-2 2012-10-29 cran (@0.1-2)
VariantAnnotation 1.20.2 2016-12-01 Bioconductor
viridis 0.3.4 2016-03-12 CRAN (R 3.3.0)
vsn 3.42.3 2016-10-24 Bioconductor
whisker 0.3-2 2013-04-28 CRAN (R 3.3.0)
withr 1.0.2 2016-06-20 CRAN (R 3.3.0)
wordcloud 2.5 2014-06-13 CRAN (R 3.3.0)
XML 3.98-1.5 2016-11-10 CRAN (R 3.3.2)
xml2 1.1.1 2017-01-24 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
zoo 1.7-14 2016-12-16 CRAN (R 3.3.2)