R_PACKAGES/3.6.0

As of 2019-05-14 there are a total of 17257 packages available. This includes 13769 CRAN packages installed, out of 14178 available; and 3031 BioConductor-specific packages installed, out of 3079 available. These R packages are available as part of the R_packages/3.6.0 module as installed on rackham, irma, bianca and snowy, which requires and loads the R/3.6.0 module.  When the R_packages/3.5.2 module is loaded, it adds a directory to the R_LIBS_SITE environment variable.  Within R, these packages will be available via library(package-name).

See module help R_packages/3.6.0 for more information.

R_PACKAGES/3.5.2

As of 2019-02-08 there are a total of 16642 packages available. This includes 13355 CRAN packages installed, out of 13683 available; and 2933 BioConductor-specific packages installed, out of 2959 available. These R packages are available as part of the R_packages/3.5.2 module as installed on rackham, irma, bianca and snowy, which requires and loads the R/3.5.2 module.  When the R_packages/3.5.2 module is loaded, it adds a directory to the R_LIBS_SITE environment variable.  Within R, these packages will be available via library(package-name).

See module help R_packages/3.5.2 for more information.

R_PACKAGES/3.5.0

With its 3.5.0 version, R_packages now attempts to install all available R packages from both CRAN and BioConductor.

As of 2018-06-26 there are a total of 14532 packages available. This includes 11734 CRAN packages installed, out of 12867 available; and 2798 BioConductor-specific packages installed, out of 2843 available. These R packages are available as part of the R_packages/3.5.0 module as installed on rackham, irma, bianca and snowy, which requires and loads the R/3.5.0 module.  When the R_packages/3.5.0 module is loaded, it adds a directory to the R_LIBS_SITE environment variable.  Within R, these packages will be available via library(package-name).

See module help R_packages/3.5.0 for more information.

R_packages/3.4.3

The following R packages are available as part of the R_packages/3.4.3 module as installed on rackham, irma and bianca, which requires and loads the R/3.4.3 module.  When the R_packages/3.4.3 module is loaded, it adds a directory to the R_LIBS_SITE environment variable.  Within R, these packages will be available via library(package-name).

Note the list of package names is sorted case-insensitive.

Package Version
abind 1.4-5
acepack 1.4.1
ade4 1.7-10
ade4TkGUI 0.2-9
adegenet 2.1.0
adegraphics 1.0-9
adephylo 1.1-11
affy 1.56.0
affyio 1.48.0
airway 0.112.0
akima 0.6-2
alr4 1.0.5
amap 0.8-14
AMOUNTAIN 1.4.0
annotate 1.56.1
AnnotationDbi 1.40.0
AnnotationFilter 1.2.0
AnnotationForge 1.20.0
AnnotationHub 2.10.1
ape 5.0
apeglm 1.0.3
ArgumentCheck 0.10.2
aroma.light 3.8.0
ASCAT 2.5
ashr 2.0.5
assertthat 0.2.0
backports 1.1.2
base64 2.0
base64enc 0.1-3
BatchJobs 1.7
bayesplot 1.4.0
baySeq 2.12.0
BBmisc 1.11
bbmle 1.0.20
bdsmatrix 1.3-3
beachmat 1.0.2
beadarray 2.28.0
BeadDataPackR 1.30.0
beanplot 1.2
beeswarm 0.2.3
BH 1.65.0-1
BiasedUrn 1.07
bigRR 1.3-10
bindr 0.1
bindrcpp 0.2
Biobase 2.38.0
BiocGenerics 0.24.0
BiocInstaller 1.28.0
BiocParallel 1.12.0
BiocStyle 2.6.1
biocViews 1.46.0
biomaRt 2.34.2
biomformat 1.6.0
Biostrings 2.46.0
biovizBase 1.26.0
bit 1.1-12
bit64 0.9-7
bitops 1.0-6
bladderbatch 1.16.0
blob 1.1.0
bold 0.5.0
bookdown 0.5
brew 1.0-6
brglm 0.6.1
broom 0.4.3
BSgenome 1.46.0
BSgenome.Celegans.UCSC.ce10 1.4.0
BSgenome.Drerio.UCSC.danRer7 1.4.0
BSgenome.Ecoli.NCBI.20080805 1.3.1000
BSgenome.Hsapiens.UCSC.hg19 1.4.0
bsseq 1.14.0
bumphunter 1.20.0
calibrate 1.7.2
car 2.1-6
carData 3.0-0
caret 6.0-78
Category 2.44.0
caTools 1.17.1
ChAMP 2.9.10
ChAMPdata 2.10.0
checkmate 1.8.5
chimeraviz 1.4.3
ChIPpeakAnno 3.12.4
ChIPQC 1.14.0
chipseq 1.28.0
chron 2.3-52
circlize 0.4.3
CircStats 0.2-4
circular 0.4-93
cli 1.0.0
clue 0.3-55
cmprsk 2.2-7
coda 0.19-1
colorspace 1.3-2
colourpicker 1.0
combinat 0.0-8
commonmark 1.4
CompQuadForm 1.4.3
corpcor 1.6.9
corrplot 0.84
covr 3.0.1
cowplot 0.9.2
crayon 1.3.4
crosstalk 1.0.0
crul 0.5.0
csaw 1.12.0
curl 3.1
CVST 0.2-1
cvTools 0.3.2
d3heatmap 0.6.1.1
DAAG 1.22
dada2 1.6.0
data.table 1.10.4-3
DatABEL 0.9-6
DBI 0.7
dbplyr 1.2.0
ddalpha 1.3.1
DDRTree 0.1.5
debugme 1.1.0
DelayedArray 0.4.1
deldir 0.1-14
dendextend 1.6.0
DendSer 1.0.1
densityClust 0.3
DEoptimR 1.0-8
desc 1.1.1
DESeq 1.30.0
DESeq2 1.18.1
deSolve 1.20
destiny 2.6.1
devtools 1.13.4
DEXSeq 1.24.2
dfoptim 2018.2-1
dichromat 2.0-0
DiffBind 2.6.6
digest 0.6.14
dimRed 0.1.0
diptest 0.75-7
DMRcate 1.14.0
DMRcatedata 1.14.0
DNAcopy 1.52.0
doParallel 1.0.11
doRNG 1.6.6
dotCall64 0.9-5.2
dplyr 0.7.4
DRR 0.0.3
DSS 2.26.0
DT 0.2
dtplyr 0.0.2
dygraphs 1.1.1.4
dynamicTreeCut 1.63-1
e1071 1.6-8
ecodist 2.0.1
edgeR 3.20.7
effects 4.0-0
ellipse 0.4.1
emdbook 1.3.9
emojifont 0.5.1
EMT 1.1
EnsDb.Hsapiens.v75 2.99.0
EnsDb.Hsapiens.v79 2.99.0
ensembldb 2.2.0
Epi 2.28
epitools 0.5-10
estimability 1.2
etm 0.6-2
etrunct 0.1
evaluate 0.10.1
exactRankTests 0.8-29
expm 0.999-2
expsmooth 2.3
FactoMineR 1.39
fastcluster 1.1.24
fastICA 1.2-1
fastmatch 1.1-0
FDb.InfiniumMethylation.hg19 2.2.0
fdrtool 1.2.15
FEM 3.6.0
fit.models 0.5-14
flashClust 1.01-2
flexmix 2.3-14
FlowSorted.Blood.450k 1.16.0
FNN 1.1
foreach 1.4.4
forecast 8.2
formattable 0.2.0.1
Formula 1.2-2
fpc 2.1-11
fracdiff 1.4-2
fts 0.9.9
futile.logger 1.4.3
futile.options 1.0.0
gam 1.14-4
gapminder 0.3.0
gclus 1.3.1
gdata 2.18.0
gdsfmt 1.14.1
gdtools 0.1.6
gee 4.13-19
geiger 2.0.6
GenABEL 1.8-0
GenABEL.data 1.0.0
genefilter 1.60.0
geneLenDataBase 1.14.0
GeneOverlap 1.14.0
geneplotter 1.56.0
genetics 1.3.8.1
GenomeInfoDb 1.14.0
GenomeInfoDbData 1.0.0
GenomicAlignments 1.14.1
GenomicFeatures 1.30.0
GenomicFiles 1.14.0
GenomicRanges 1.30.1
GEOquery 2.46.15
getopt 1.20.1
GGally 1.3.2
ggbeeswarm 0.6.0
ggplot2 2.2.1
ggplot2movies 0.0.1
ggpubr 0.1.6
ggrepel 0.7.0
ggsci 2.8
ggsignif 0.4.0
ggtree 1.10.2
git2r 0.21.0
Glimma 1.6.0
glmnet 2.0-13
GlobalOptions 0.0.12
glue 1.2.0
gmailr 0.7.1
gmodels 2.16.2
GO.db 3.5.0
googleVis 0.6.2
goseq 1.30.0
GOstats 2.44.0
gower 0.1.2
gplots 3.0.1
graph 1.56.0
gridBase 0.4-7
gridExtra 2.3
grImport 0.9-0
gsalib 2.1
GSEABase 1.40.1
gsl 1.9-10.3
gtable 0.2.0
gtools 3.5.0
Gviz 1.22.2
haplo.stats 1.7.7
HDF5Array 1.6.0
heatmap3 1.1.1
heatmaply 0.14.0
hexbin 1.27.2
hflights 0.1
hglm 2.1-1
hglm.data 1.0-0
hgu95av2.db 3.2.3
hierfstat 0.04-22
highr 0.6
Hmisc 4.1-1
hms 0.4.0
hom.Hs.inp.db 3.1.2
HSMMSingleCell 0.112.0
htmlTable 1.11.2
htmltools 0.3.6
htmlwidgets 1.0
htSeqTools 1.26.0
httpcode 0.2.0
httpuv 1.3.5
httr 1.3.1
hunspell 2.9
hwriter 1.3.2
ibdreg 0.2.5
idr 1.2
igraph 1.1.2
igraph0 0.5.7
igraphdata 1.0.1
IHW 1.6.0
Illumina450ProbeVariants.db 1.14.0
IlluminaHumanMethylation450kanno.ilmn12.hg19 0.6.0
IlluminaHumanMethylation450kmanifest 0.4.0
IlluminaHumanMethylationEPICanno.ilm10b2.hg19 0.6.0
IlluminaHumanMethylationEPICmanifest 0.3.0
illuminaio 0.20.0
impute 1.52.0
inline 0.3.14
interactiveDisplayBase 1.16.0
ipred 0.9-6
IRanges 2.12.0
IRdisplay 0.4.4
irlba 2.3.2
isva 1.9
iterators 1.0.9
itertools 0.1-3
JADE 2.0-1
jose 0.1
jpeg 0.1-8
jsonlite 1.5
kableExtra 0.7.0
KEGG.db 3.2.3
kernlab 0.9-25
km.ci 0.5-2
KMsurv 0.1-5
knitr 1.18
labeling 0.3
laeken 0.4.6
Lahman 6.0-0
lambda.r 1.2
latticeExtra 0.6-28
lava 1.6
lazyeval 0.2.1
leaps 3.0
LearnBayes 2.15
limma 3.34.5
limSolve 1.5.5.3
lintr 1.0.2
lme4 1.1-15
lmerTest 2.0-36
lmtest 0.9-35
locfit 1.5-9.1
loo 1.1.0
lpSolve 5.6.13
lpsymphony 1.7.1
lsmeans 2.27-61
lubridate 1.7.1
lumi 2.30.0
lumiBarnes 1.18.0
lumiHumanAll.db 1.22.0
lumiHumanIDMapping 1.10.1
MAd 0.8-2
magick 1.8
magrittr 1.5
manhattanly 0.2.0
mapdata 2.2-6
mapproj 1.2-5
maps 3.2.0
maptools 0.9-2
markdown 0.8
marray 1.56.0
MatrixModels 0.4-1
matrixStats 0.52.2
maxLik 1.3-4
maxstat 0.7-25
mclust 5.4
memoise 1.1.0
memuse 4.0-0
MetABEL 0.2-0
metafor 2.0-0
metagenomeSeq 1.20.1
metap 0.9
methylumi 2.24.1
mice 2.46.0
microbenchmark 1.4-3
mime 0.5
minfi 1.24.0
minfiData 0.24.0
minfiDataEPIC 1.4.0
miniUI 0.1.1
minqa 1.2.4
miscTools 0.6-22
missMDA 1.11
missMethyl 1.12.0
mixOmics 6.3.1
mnormt 1.5-5
MODA 1.4.0
ModelMetrics 1.1.0
modeltools 0.2-21
mondate 0.10.01.02
monocle 2.6.1
motifStack 1.22.2
MotIV 1.34.0
multcomp 1.4-8
MultiAssayExperiment 1.4.9
multtest 2.34.0
munsell 0.4.3
mvoutlier 2.0.8
mvtnorm 1.0-6
nanotime 0.2.0
natserv 0.1.4
naturalsort 0.1.3
ncbit 2013.03.29
nleqslv 3.3.1
nloptr 1.0.4
NMF 0.20.6
nor1mix 1.2-3
Nozzle.R1 1.1-1
numDeriv 2016.8-1
nycflights13 0.2.2
openssl 0.9.9
optparse 1.4.4
org.At.tair.db 3.5.0
org.Ce.eg.db 3.5.0
org.Hs.eg.db 3.5.0
org.Mm.eg.db 3.5.0
org.Sc.sgd.db 3.5.0
OrganismDbi 1.20.0
OxyBS 1.5
packrat 0.4.8-1
pamr 1.55
parathyroidSE 1.16.0
pasilla 1.6.0
pbapply 1.3-4
pbkrtest 0.4-7
PBSmodelling 2.68.6
pca3d 0.10
pcaPP 1.9-73
pdftools 1.5
pegas 0.10
permute 0.9-4
phangorn 2.3.1
pheatmap 1.0.8
phylobase 0.8.4
phyloseq 1.22.3
picante 1.6-2
pillar 1.1.0
pinfsc50 1.1.0
pinp 0.0.4
pixmap 0.4-11
pkgconfig 2.0.1
pkgKitten 0.1.4
pkgmaker 0.22
PKI 0.1-5.1
plm 1.6-6
plogr 0.1-1
plotly 4.7.1
plotrix 3.7
plotwidgets 0.4
pls 2.6-0
plyr 1.8.4
png 0.1-7
polspline 1.1.12
poppr 2.6.1
prabclus 2.2-6
pracma 2.1.1
praise 1.0.0
PredictABEL 1.2-2
preprocessCore 1.40.0
prettydoc 0.2.1
prettyunits 1.0.2
processx 2.0.0.1
prodlim 1.6.1
profdpm 3.3
profileModel 0.5-9
progress 1.1.2
ProtGenerics 1.10.0
proto 1.0.0
proxy 0.4-21
pscl 1.5.2
psych 1.7.8
purrr 0.2.4
pvclust 2.0-0
qap 0.1-1
qlcMatrix 0.9.5
qqman 0.1.4
quadprog 1.5-5
quantmod 0.4-12
quantreg 5.34
qvalue 2.10.0
R.cache 0.13.0
R.methodsS3 1.7.1
R.oo 1.21.0
R.rsp 0.42.0
R.utils 2.6.0
R6 2.2.2
RaggedExperiment 1.2.5
randomForest 4.6-12
RANN 2.5.1
rappdirs 0.3.1
rARPACK 0.11-0
raster 2.6-7
rbenchmark 1.0.0
RBGL 1.54.0
RCircos 1.2.0
RColorBrewer 1.1-2
Rcpp 0.12.15
RcppArmadillo 0.8.300.1.0
RcppCCTZ 0.2.3
RcppEigen 0.3.3.3.1
RcppGSL 0.3.3
RcppParallel 4.3.20
RcppRoll 0.2.2
RCurl 1.95-4.10
reactome.db 1.62.0
readr 1.1.1
recipes 0.1.2
regioneR 1.10.0
registry 0.5
rentrez 1.1.0
repr 0.12.0
reshape 0.8.7
reshape2 1.4.3
rex 1.1.2
rGADEM 2.26.0
rgdal 1.2-18
rgl 0.99.9
Rgraphviz 2.22.0
rhdf5 2.22.0
Rhdf5lib 1.0.0
Rhtslib 1.10.0
ritis 0.7.0
rjson 0.2.15
RJSONIO 1.3-0
rlang 0.1.6
rmarkdown 1.8
rms 5.1-2
RMySQL 0.10.14
rncl 0.8.2
RNeXML 2.0.8
rngtools 1.2.4
robCompositions 2.0.6
robust 0.4-18
robustbase 0.92-8
ROC 1.54.0
ROCR 1.0-7
rotl 3.0.3
roxygen2 6.0.1
RPMM 1.25
RPostgreSQL 0.6-2
rprojroot 1.3-2
rrcov 1.4-3
rredlist 0.4.0
Rsamtools 1.30.0
rsconnect 0.8.5
RSpectra 0.12-0
RSQLite 2.0
rstan 2.17.3
rstantools 1.4.0
rstudioapi 0.7
rsvg 1.1
RTCGAToolbox 2.8.0
rticles 0.4.1
rtracklayer 1.38.2
Rtsne 0.13
RUnit 0.4.31
ruv 0.9.7
rvcheck 0.0.9
rversions 1.0.3
rvest 0.3.2
S4Vectors 0.16.0
samr 2.0
sandwich 2.4-0
scales 0.5.0
scater 1.6.2
scatterplot3d 0.3-40
scran 1.6.6
segmented 0.5-3.0
selectr 0.3-1
sendmailR 1.2-1
seqinr 3.4-5
seqLogo 1.44.0
seriation 1.2-2
sfsmisc 1.1-1
sgeostat 1.0-27
shape 1.4.3
shiny 1.0.5
shinydashboard 0.6.1
shinyjs 1.0
shinythemes 1.1.1
ShortRead 1.36.0
showtext 0.5-1
showtextdb 2.0
siggenes 1.52.0
SingleCellExperiment 1.0.0
slam 0.1-42
smoother 1.1
snow 0.4-2
SNPRelate 1.12.2
solrium 1.0.0
sourcetools 0.1.6
sp 1.2-7
spam 2.1-2
SparseM 1.77
spData 0.2.6.9
spdep 0.7-4
spelling 1.1
sphet 1.6
splancs 2.01-40
splm 1.4-10
SQUAREM 2017.10-1
sROC 0.1-2
StanHeaders 2.17.2
statmod 1.4.30
stringdist 0.9.4.6
stringi 1.1.6
stringr 1.2.0
strucchange 1.5-1
subplex 1.4-1
SummarizedExperiment 1.8.1
survey 3.33
survminer 0.4.1
survMisc 0.5.4
sva 3.26.0
svglite 1.2.1
sysfonts 0.7.2
systemPipeR 1.12.0
tagcloud 0.6
taxize 0.9.0
TCC 1.18.0
testthat 2.0.0
TH.data 1.0-8
threejs 0.3.1
tibble 1.4.2
tidyr 0.7.2
tidyselect 0.2.3
tiff 0.1-5
timeDate 3042.101
timeSeries 3042.102
tis 1.34
tkrplot 0.0-23
tmod 0.31
trackViewer 1.14.0
treeio 1.2.1
triebeard 0.3.0
trimcluster 0.1-2
tripack 1.3-8
truncnorm 1.0-7
tseries 0.10-42
TSP 1.1-5
TTR 0.23-2
tufte 0.2
tweeDEseqCountData 1.16.0
TxDb.Celegans.UCSC.ce6.ensGene 3.2.2
TxDb.Dmelanogaster.UCSC.dm3.ensGene 3.2.2
TxDb.Hsapiens.UCSC.hg18.knownGene 3.2.2
TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
TxDb.Hsapiens.UCSC.hg38.knownGene 3.4.0
TxDb.Mmusculus.UCSC.mm10.knownGene 3.4.0
TxDb.Mmusculus.UCSC.mm9.knownGene 3.2.2
TxDb.Rnorvegicus.UCSC.rn4.ensGene 3.2.2
tximport 1.6.0
tximportData 1.6.0
ucminf 1.1-4
UpSetR 1.3.3
urltools 1.7.0
utf8 1.1.3
uuid 0.1-2
VariantAnnotation 1.24.5
vcd 1.4-4
vcfR 1.6.0
vegan 2.4-5
VennDiagram 1.6.18
VGAM 1.0-4
VIM 4.7.0
vipor 0.4.5
viridis 0.4.1
viridisLite 0.2.0
vsn 3.46.0
wateRmelon 1.22.1
waveslim 1.7.5
webp 0.4
webshot 0.5.0
webutils 0.6
WGCNA 1.61
whisker 0.3-2
WikidataR 1.4.0
WikipediR 1.5.0
wikitaxa 0.2.0
withr 2.1.1
worrms 0.2.0
XML 3.98-1.9
xml2 1.1.1
xtable 1.8-2
xts 0.10-1
XVector 0.18.0
yaml 2.1.16
zebrafishRNASeq 0.112.0
zipcode 1.0
zlibbioc 1.24.0
zoo 1.8-1

R_packages/3.4.0

The following R packages are available as part of the R_packages/3.4.0 module, which requires and loads the R/3.4.0 module.  When the R_packages/3.4.0 module is loaded, it adds a directory to the R_LIBS_SITE environment variable.  Within R, these packages will be available via library(package-name).

Package Version
AMOUNTAIN 1.2.0
ASCAT 2.4.4
AnnotationDbi 1.38.2
AnnotationFilter 1.0.0
AnnotationForge 1.18.2
AnnotationHub 2.8.3
BBmisc 1.11
BH 1.65.0-1
BSgenome 1.44.2
BatchJobs 1.6
BiasedUrn 1.07
Biobase 2.36.2
BiocGenerics 0.22.1
BiocInstaller 1.26.1
BiocParallel 1.10.1
Biostrings 2.44.2
Category 2.42.1
ChIPQC 1.12.3
ChIPpeakAnno 3.10.2
DBI 0.7
DESeq 1.28.0
DESeq2 1.16.1
DEXSeq 1.22.0
DEoptimR 1.0-8
DT 0.2
DelayedArray 0.2.7
DiffBind 2.4.8
EMT 1.1
FNN 1.1
Formula 1.2-2
GO.db 3.4.1
GOstats 2.42.0
GSEABase 1.38.2
GenomeInfoDb 1.12.3
GenomeInfoDbData 0.99.0
GenomicAlignments 1.12.2
GenomicFeatures 1.28.5
GenomicRanges 1.28.6
Glimma 1.4.0
Gviz 1.20.0
Hmisc 4.0-3
IRanges 2.10.5
Lahman 6.0-0
LearnBayes 2.15
MODA 1.2.0
MultiAssayExperiment 1.2.1
NMF 0.20.6
Nozzle.R1 1.1-1
ProtGenerics 1.8.0
R6 2.2.2
RBGL 1.52.0
RColorBrewer 1.1-2
RCurl 1.95-4.8
RJSONIO 1.3-0
ROC 1.52.0
RSQLite 2.0
RSpectra 0.12-0
Rcpp 0.12.13
RcppArmadillo 0.8.100.1.0
RcppEigen 0.3.3.3.0
RcppParallel 4.3.20
Rhtslib 1.8.0
Rsamtools 1.28.0
S4Vectors 0.14.7
ShortRead 1.34.2
StanHeaders 2.16.0-1
SummarizedExperiment 1.6.5
TCC 1.16.0
TxDb.Celegans.UCSC.ce6.ensGene 3.2.2
TxDb.Dmelanogaster.UCSC.dm3.ensGene 3.2.2
TxDb.Hsapiens.UCSC.hg18.knownGene 3.2.2
TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
TxDb.Hsapiens.UCSC.hg38.knownGene 3.4.0
TxDb.Mmusculus.UCSC.mm10.knownGene 3.4.0
TxDb.Mmusculus.UCSC.mm9.knownGene 3.2.2
TxDb.Rnorvegicus.UCSC.rn4.ensGene 3.2.2
UpSetR 1.3.3
VariantAnnotation 1.22.3
VennDiagram 1.6.17
WGCNA 1.61
XML 3.98-1.9
XVector 0.16.0
abind 1.4-5
acepack 1.4.1
ade4 1.7-8
adegenet 2.1.0
akima 0.6-2
amap 0.8-14
annotate 1.54.0
ape 4.1
assertthat 0.2.0
backports 1.1.1
base64enc 0.1-3
baySeq 2.10.0
beeswarm 0.2.3
bindr 0.1
bindrcpp 0.2
biomaRt 2.32.1
biomformat 1.4.0
biovizBase 1.24.0
bit 1.1-12
bit64 0.9-7
bitops 1.0-6
blob 1.1.0
brew 1.0-6
caTools 1.17.1
checkmate 1.8.5
chipseq 1.26.1
chron 2.3-51
coda 0.19-1
colorspace 1.3-2
combinat 0.0-8
corpcor 1.6.9
crayon 1.3.4
csaw 1.10.0
curl 3.0
dada2 1.4.0
data.table 1.10.4-3
deSolve 1.20
deldir 0.1-14
dendextend 1.5.2
dichromat 2.0-0
digest 0.6.12
diptest 0.75-7
doParallel 1.0.11
dplyr 0.7.4
dynamicTreeCut 1.63-1
ecodist 2.0.1
edgeR 3.18.1
ellipse 0.3-8
ensembldb 2.0.4
evaluate 0.10.1
expm 0.999-2
fail 1.3
fastcluster 1.1.24
filehash 2.4-1
fit.models 0.5-14
flexmix 2.3-14
foreach 1.4.3
formatR 1.5
fpc 2.1-10
futile.logger 1.4.3
futile.options 1.0.0
gdata 2.18.0
gee 4.13-19
geiger 2.0.6
geneLenDataBase 1.12.0
genefilter 1.58.1
geneplotter 1.54.0
getopt 1.20.0
ggbeeswarm 0.6.0
ggplot2 2.2.1
ggrepel 0.7.0
ggtree 1.8.2
glue 1.2.0
gmodels 2.16.2
goseq 1.28.0
gplots 3.0.1
graph 1.54.0
gridBase 0.4-7
gridExtra 2.3
gtable 0.2.0
gtools 3.5.0
hexbin 1.27.1
hflights 0.1
highr 0.6
htSeqTools 1.24.0
htmlTable 1.9
htmltools 0.3.6
htmlwidgets 0.9
httpuv 1.3.5
httr 1.3.1
hwriter 1.3.2
idr 1.2
igraph 1.1.2
igraph0 0.5.7
impute 1.50.1
inline 0.3.14
interactiveDisplayBase 1.14.0
irlba 2.3.1
iterators 1.0.8
jpeg 0.1-8
jsonlite 1.5
kernlab 0.9-25
knitr 1.17
labeling 0.3
lambda.r 1.2
latticeExtra 0.6-28
lazyeval 0.2.1
limma 3.32.10
lme4 1.1-14
lmerTest 2.0-33
locfit 1.5-9.1
magrittr 1.5
maps 3.2.0
markdown 0.8
matrixStats 0.52.2
mclust 5.3
memoise 1.1.0
memuse 3.0-1
microbenchmark 1.4-2.1
mime 0.5
minqa 1.2.4
mixOmics 6.3.0
modeltools 0.2-21
multtest 2.32.0
munsell 0.4.3
mvtnorm 1.0-6
naturalsort 0.1.3
ncbit 2013.03.29
nloptr 1.0.4
openssl 0.9.7
optparse 1.4.4
org.Mm.eg.db 3.4.1
pca3d 0.10
pcaPP 1.9-72
permute 0.9-4
pheatmap 1.0.8
phyloseq 1.20.0
picante 1.6-2
pinfsc50 1.1.0
pkgconfig 2.0.1
pkgmaker 0.22
plogr 0.1-1
plotrix 3.6-6
plotwidgets 0.4
plyr 1.8.4
png 0.1-7
prabclus 2.2-6
praise 1.0.0
preprocessCore 1.38.1
proto 1.0.0
purrr 0.2.4
pvclust 2.0-0
rARPACK 0.11-0
reactome.db 1.59.1
regioneR 1.8.1
registry 0.3
reshape 0.8.7
reshape2 1.4.2
rgl 0.98.1
rhdf5 2.20.0
rjson 0.2.15
rlang 0.1.2
rmarkdown 1.6
rngtools 1.2.4
robust 0.4-18
robustbase 0.92-7
rprojroot 1.2
rrcov 1.4-3
rtracklayer 1.36.6
rvcheck 0.0.9
samr 2.0
scales 0.5.0
scater 1.4.0
scran 1.4.5
segmented 0.5-2.2
sendmailR 1.2-1
seqinr 3.4-5
shiny 1.0.5
shinydashboard 0.6.1
snow 0.4-2
snpStats 1.26.0
sourcetools 0.1.6
sp 1.2-5
spdep 0.6-15
statmod 1.4.30
stringi 1.1.5
stringr 1.2.0
subplex 1.4-1
sva 3.24.4
systemPipeR 1.10.2
tagcloud 0.6
testit 0.7
testthat 1.0.2
tibble 1.3.4
tidyr 0.7.2
tidyselect 0.2.2
tikzDevice 0.10-1
tkrplot 0.0-23
tmod 0.31
treeio 1.0.2
trimcluster 0.1-2
tximport 1.4.0
vcfR 1.5.0
vegan 2.4-4
vipor 0.4.5
viridis 0.4.0
viridisLite 0.2.0
webshot 0.4.2
whisker 0.3-2
xtable 1.8-2
yaml 2.1.14
zlibbioc 1.22.0
zoo 1.8-0

R_packages/3.3.2

The following R packages are available as part of the R_packages/3.3.2 module, which requires and loads the R/3.3.2 module.  When the R_packages/3.3.2 module is loaded, it adds a directory to the R_LIBS_SITE environment variable.  Within R, these packages will be available via library(package-name).

Package Version
ASCAT 2.4.3
AnnotationDbi 1.36.2
AnnotationHub 2.6.5
BH 1.62.0-1
BSgenome 1.42.0
BiasedUrn 1.07
Biobase 2.34.0
BiocGenerics 0.20.0
BiocInstaller 1.24.0
BiocParallel 1.8.2
Biostrings 2.42.1
DBI 0.6-1
DESeq 1.26.0
DESeq2 1.14.1
DEXSeq 1.20.2
DEoptimR 1.0-8
Formula 1.2-1
GO.db 3.4.0
GenomeInfoDb 1.10.3
GenomicAlignments 1.10.1
GenomicFeatures 1.26.4
GenomicRanges 1.26.4
Gviz 1.18.2
Hmisc 4.0-2
IRanges 2.8.2
LearnBayes 2.15
MODA 1.0.0
NMF 0.20.6
R6 2.2.0
RColorBrewer 1.1-2
RCurl 1.95-4.8
RSQLite 1.1-2
Rcpp 0.12.10
RcppArmadillo 0.7.800.2.0
RcppEigen 0.3.2.9.1
RcppParallel 4.3.20
Rsamtools 1.26.2
S4Vectors 0.12.2
ShortRead 1.32.1
SummarizedExperiment 1.4.0
VariantAnnotation 1.20.3
VennDiagram 1.6.17
WGCNA 1.51
XML 3.98-1.6
XVector 0.14.1
acepack 1.4.1
ade4 1.7-6
adegenet 2.0.1
akima 0.6-2
annotate 1.52.1
ape 4.1
assertthat 0.2.0
backports 1.0.5
base64enc 0.1-3
beeswarm 0.2.3
biomaRt 2.30.0
biovizBase 1.22.0
bitops 1.0-6
caTools 1.17.1
checkmate 1.8.2
chron 2.3-50
coda 0.19-1
colorspace 1.3-2
combinat 0.0-8
crayon 1.3.2
curl 2.5
dada2 1.2.2
data.table 1.10.4
deSolve 1.14
deldir 0.1-14
dendextend 1.5.2
dendextendRcpp 0.6.1
dichromat 2.0-0
digest 0.6.12
diptest 0.75-7
doParallel 1.0.10
dplyr 0.5.0
dynamicTreeCut 1.63-1
edgeR 3.16.5
ellipse 0.3-8
ensembldb 1.6.2
evaluate 0.10
expm 0.999-2
fastcluster 1.1.22
flexmix 2.3-13
foreach 1.4.3
fpc 2.1-10
futile.logger 1.4.3
futile.options 1.0.0
gdata 2.17.0
geiger 2.0.6
geneLenDataBase 1.10.0
genefilter 1.56.0
geneplotter 1.52.0
getopt 1.20.0
ggplot2 2.2.1
ggtree 1.6.11
gmodels 2.16.2
goseq 1.26.0
gplots 3.0.1
gridBase 0.4-7
gridExtra 2.2.1
gtable 0.2.0
gtools 3.5.0
hash 2.2.6
hexbin 1.27.1
highr 0.6
htmlTable 1.9
htmltools 0.3.5
htmlwidgets 0.8
httpuv 1.3.3
httr 1.2.1
hwriter 1.3.2
igraph 1.0.1
impute 1.48.0
interactiveDisplayBase 1.12.0
irlba 2.1.2
iterators 1.0.8
jsonlite 1.4
kernlab 0.9-25
knitr 1.15.1
labeling 0.3
lambda.r 1.1.9
latticeExtra 0.6-28
lazyeval 0.2.0
limma 3.30.13
lme4 1.1-13
lmerTest 2.0-33
locfit 1.5-9.1
magrittr 1.5
maps 3.1.1
markdown 0.8
matrixStats 0.52.2
mclust 5.2.3
memoise 1.1.0
microbenchmark 1.4-2.1
mime 0.5
minqa 1.2.4
modeltools 0.2-21
munsell 0.4.3
mvtnorm 1.0-6
naturalsort 0.1.3
ncbit 2013.03.29
nloptr 1.0.4
openssl 0.9.6
org.Mm.eg.db 3.4.0
pca3d 0.10
permute 0.9-4
picante 1.6-2
pkgmaker 0.22
plogr 0.1-1
plotrix 3.6-4
plotwidgets 0.4
plyr 1.8.4
prabclus 2.2-6
praise 1.0.0
preprocessCore 1.36.0
pvclust 2.0-0
reactome.db 1.58.0
registry 0.3
reshape2 1.4.2
rgl 0.98.1
rmarkdown 1.4
rngtools 1.2.4
robustbase 0.92-7
rprojroot 1.2
rtracklayer 1.34.2
scales 0.4.1
segmented 0.5-1.4
seqinr 3.3-6
shiny 1.0.2
snow 0.4-2
sourcetools 0.1.6
sp 1.2-4
spdep 0.6-13
statmod 1.4.29
stringi 1.1.5
stringr 1.2.0
subplex 1.2-2
sva 3.22.0
tagcloud 0.6
testthat 1.0.2
tibble 1.3.0
tidyr 0.6.1
tkrplot 0.0-23
tmod 0.31
trimcluster 0.1-2
vegan 2.4-3
viridis 0.4.0
viridisLite 0.2.0
whisker 0.3-2
xtable 1.8-2
yaml 2.1.14
zlibbioc 1.20.0
zoo 1.8-0

R_packages/3.3.1

The following R packages are available as part of the R_packages/3.3.1 module, which requires and loads the R/3.3.1 module.  When the R_packages/3.3.1 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these should be available via library(package-name).

Package Version
ASCAT 2.4.3
AnnotationDbi 1.36.0
AnnotationHub 2.6.0
BH 1.60.0-2
BSgenome 1.42.0
BiasedUrn 1.07
Biobase 2.34.0
BiocGenerics 0.20.0
BiocInstaller 1.24.0
BiocParallel 1.8.0
Biostrings 2.42.0
DBI 0.5-1
DESeq 1.26.0
DESeq2 1.14.0
DEXSeq 1.20.0
DEoptimR 1.0-6
Formula 1.2-1
GO.db 3.4.0
GenomeInfoDb 1.10.0
GenomicAlignments 1.10.0
GenomicFeatures 1.26.0
GenomicRanges 1.26.1
Gviz 1.18.0
Hmisc 3.17-4
IRanges 2.8.0
LearnBayes 2.15
NMF 0.20.6
R6 2.2.0
RColorBrewer 1.1-2
RCurl 1.95-4.8
RSQLite 1.0.0
Rcpp 0.12.7
RcppArmadillo 0.7.500.0.0
RcppEigen 0.3.2.9.0
RcppParallel 4.3.20
Rsamtools 1.26.1
S4Vectors 0.12.0
ShortRead 1.32.0
SummarizedExperiment 1.4.0
VariantAnnotation 1.20.0
VennDiagram 1.6.17
XML 3.98-1.4
XVector 0.14.0
acepack 1.4.0
ade4 1.7-4
adegenet 2.0.1
akima 0.5-12
annotate 1.52.0
ape 3.5
assertthat 0.1
base64enc 0.1-3
beeswarm 0.2.3
biomaRt 2.30.0
biovizBase 1.22.0
bitops 1.0-6
caTools 1.17.1
chron 2.3-47
coda 0.18-1
colorspace 1.2-7
combinat 0.0-8
crayon 1.3.2
curl 2.2
dada2 1.2.0
data.table 1.9.6
deSolve 1.14
deldir 0.1-12
dendextend 1.3.0
dendextendRcpp 0.6.1
dichromat 2.0-0
digest 0.6.10
diptest 0.75-7
doParallel 1.0.10
dplyr 0.5.0
edgeR 3.16.0
ellipse 0.3-8
ensembldb 1.6.0
evaluate 0.10
flexmix 2.3-13
foreach 1.4.3
formatR 1.4
fpc 2.1-10
futile.logger 1.4.3
futile.options 1.0.0
gdata 2.17.0
geiger 2.0.6
geneLenDataBase 1.10.0
genefilter 1.56.0
geneplotter 1.52.0
getopt 1.20.0
ggplot2 2.1.0
ggtree 1.6.0
gmodels 2.16.2
goseq 1.26.0
gplots 3.0.1
gridBase 0.4-7
gridExtra 2.2.1
gtable 0.2.0
gtools 3.5.0
hexbin 1.27.1
highr 0.6
htmltools 0.3.5
htmlwidgets 0.8
httpuv 1.3.3
httr 1.2.1
hwriter 1.3.2
igraph 1.0.1
interactiveDisplayBase 1.12.0
irlba 2.1.2
iterators 1.0.8
jsonlite 1.1
kernlab 0.9-25
knitr 1.14
labeling 0.3
lambda.r 1.1.9
latticeExtra 0.6-28
lazyeval 0.2.0
limma 3.30.0
lme4 1.1-12
lmerTest 2.0-32
locfit 1.5-9.1
magrittr 1.5
maps 3.1.1
markdown 0.7.7
matrixStats 0.51.0
mclust 5.2
microbenchmark 1.4-2.1
mime 0.5
minqa 1.2.4
modeltools 0.2-21
munsell 0.4.3
mvtnorm 1.0-5
naturalsort 0.1.3
ncbit 2013.03.29
nloptr 1.0.4
openssl 0.9.4
org.Mm.eg.db 3.4.0
pca3d 0.10
permute 0.9-4
picante 1.6-2
pkgmaker 0.22
plotrix 3.6-3
plotwidgets 0.4
plyr 1.8.4
prabclus 2.2-6
praise 1.0.0
pvclust 2.0-0
reactome.db 1.55.0
registry 0.3
reshape2 1.4.2
rgl 0.98.1
rmarkdown 1.1
rngtools 1.2.4
robustbase 0.92-6
rtracklayer 1.34.0
scales 0.4.0
segmented 0.5-1.4
seqinr 3.3-3
shiny 0.14.1
snow 0.4-2
sourcetools 0.1.5
sp 1.2-3
spdep 0.6-8
statmod 1.4.26
stringi 1.1.2
stringr 1.1.0
subplex 1.1-6
sva 3.22.0
tagcloud 0.6
testthat 1.0.2
tibble 1.2
tidyr 0.6.0
tkrplot 0.0-23
tmod 0.31
trimcluster 0.1-2
vegan 2.4-1
whisker 0.3-2
xtable 1.8-2
yaml 2.1.13
zlibbioc 1.20.0
zoo 1.7-13

R_packages/3.3.0

The following R packages are available as part of the R_packages/3.3.0 module, which requires and loads the R/3.3.0 module.  When the R_packages/3.3.0 module is loaded, it adds a directory to the R_LIBS_SITE environment variable. Within R, these should be available via library(package-name).

Package Version
AnnotationDbi 1.34.4
AnnotationHub 2.4.2
BH 1.60.0-2
BSgenome 1.40.1
BiasedUrn 1.07
Biobase 2.32.0
BiocGenerics 0.18.0
BiocInstaller 1.22.3
BiocParallel 1.6.6
Biostrings 2.40.2
DBI 0.5-1
DESeq 1.24.0
DESeq2 1.12.4
DEXSeq 1.18.4
DEoptimR 1.0-6
Formula 1.2-1
GO.db 3.3.0
GenomeInfoDb 1.8.7
GenomicAlignments 1.8.4
GenomicFeatures 1.24.5
GenomicRanges 1.24.3
Gviz 1.16.5
Hmisc 3.17-4
IRanges 2.6.1
LearnBayes 2.15
NMF 0.20.6
R6 2.2.0
RColorBrewer 1.1-2
RCurl 1.95-4.8
RSQLite 1.0.0
Rcpp 0.12.7
RcppArmadillo 0.7.400.2.0
RcppEigen 0.3.2.9.0
Rhtslib 1.4.3
Rsamtools 1.24.0
S4Vectors 0.10.3
ShortRead 1.30.0
SummarizedExperiment 1.2.3
VariantAnnotation 1.18.7
VennDiagram 1.6.17
XML 3.98-1.4
XVector 0.12.1
acepack 1.3-3.3
ade4 1.7-4
adegenet 2.0.1
akima 0.5-12
annotate 1.50.1
ape 3.5
assertthat 0.1
base64enc 0.1-3
beeswarm 0.2.3
biomaRt 2.28.0
biovizBase 1.20.0
bitops 1.0-6
caTools 1.17.1
chron 2.3-47
coda 0.18-1
colorspace 1.2-7
combinat 0.0-8
crayon 1.3.2
curl 2.1
dada2 1.0.3
data.table 1.9.6
deSolve 1.14
deldir 0.1-12
dendextend 1.3.0
dendextendRcpp 0.6.1
dichromat 2.0-0
digest 0.6.10
diptest 0.75-7
doParallel 1.0.10
dplyr 0.5.0
edgeR 3.14.0
ellipse 0.3-8
ensembldb 1.4.7
evaluate 0.10
fields 8.4-1
flexmix 2.3-13
foreach 1.4.3
formatR 1.4
fpc 2.1-10
futile.logger 1.4.3
futile.options 1.0.0
gdata 2.17.0
geiger 2.0.6
geneLenDataBase 1.8.0
genefilter 1.54.2
geneplotter 1.50.0
getopt 1.20.0
ggplot2 2.1.0
gmodels 2.16.2
goseq 1.24.0
gplots 3.0.1
gridBase 0.4-7
gridExtra 2.2.1
gtable 0.2.0
gtools 3.5.0
hexbin 1.27.1
highr 0.6
htmltools 0.3.5
htmlwidgets 0.8
httpuv 1.3.3
httr 1.2.1
hwriter 1.3.2
igraph 1.0.1
interactiveDisplayBase 1.10.3
irlba 2.1.2
iterators 1.0.8
jsonlite 1.1
kernlab 0.9-25
knitr 1.14
labeling 0.3
lambda.r 1.1.9
latticeExtra 0.6-28
lazyeval 0.2.0
limma 3.28.21
lme4 1.1-12
lmerTest 2.0-32
locfit 1.5-9.1
magrittr 1.5
maps 3.1.1
markdown 0.7.7
matrixStats 0.51.0
mclust 5.2
memoise 1.0.0
microbenchmark 1.4-2.1
mime 0.5
minqa 1.2.4
modeltools 0.2-21
munsell 0.4.3
mvtnorm 1.0-5
naturalsort 0.1.3
ncbit 2013.03.29
nloptr 1.0.4
openssl 0.9.4
org.Mm.eg.db 3.3.0
pca3d 0.10
permute 0.9-4
picante 1.6-2
pkgmaker 0.22
plotrix 3.6-3
plotwidgets 0.4
plyr 1.8.4
prabclus 2.2-6
praise 1.0.0
pvclust 2.0-0
reactome.db 1.55.0
registry 0.3
reshape2 1.4.1
rgl 0.98.1
rmarkdown 1.1
rngtools 1.2.4
robustbase 0.92-6
rtracklayer 1.32.2
scales 0.4.0
segmented 0.5-1.4
seqinr 3.3-3
shiny 0.14.1
snow 0.4-2
sourcetools 0.1.5
sp 1.2-3
spam 1.4-0
spdep 0.6-8
statmod 1.4.26
stringi 1.1.2
stringr 1.1.0
subplex 1.1-6
sva 3.20.0
tagcloud 0.6
testthat 1.0.2
tibble 1.2
tidyr 0.6.0
tkrplot 0.0-23
tmod 0.31
trimcluster 0.1-2
vegan 2.4-1
whisker 0.3-2
xtable 1.8-2
yaml 2.1.13
zlibbioc 1.18.0
zoo 1.7-13