Uppsala Multidisciplinary Center for Advanced Computational Science

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).

PackageVersion
AMOUNTAIN1.4.0
ASCAT2.5
AnnotationDbi1.40.0
AnnotationFilter1.2.0
AnnotationForge1.20.0
AnnotationHub2.10.1
BBmisc1.11
BH1.62.0-1
BSgenome1.46.0
BSgenome.Celegans.UCSC.ce101.4.0
BSgenome.Drerio.UCSC.danRer71.4.0
BSgenome.Ecoli.NCBI.200808051.3.1000
BSgenome.Hsapiens.UCSC.hg191.4.0
BatchJobs1.7
BiasedUrn1.07
Biobase2.38.0
BiocGenerics0.24.0
BiocInstaller1.28.0
BiocParallel1.12.0
BiocStyle2.6.1
Biostrings2.46.0
CVST0.2-1
Category2.44.0
ChIPQC1.14.0
ChIPpeakAnno3.12.3
CircStats0.2-4
DAAG1.22
DBI0.7
DDRTree0.1.5
DESeq1.30.0
DESeq21.18.1
DEXSeq1.24.1
DEoptimR1.0-8
DRR0.0.2
DT0.2
DelayedArray0.4.1
DendSer1.0.1
DiffBind2.6.1
EMT1.1
EnsDb.Hsapiens.v752.99.0
EnsDb.Hsapiens.v792.99.0
FNN1.1
Formula1.2-2
GGally1.3.2
GO.db3.5.0
GOstats2.44.0
GSEABase1.40.1
GenomeInfoDb1.14.0
GenomeInfoDbData0.99.1
GenomicAlignments1.14.1
GenomicFeatures1.30.0
GenomicFiles1.14.0
GenomicRanges1.30.0
Glimma1.6.0
GlobalOptions0.0.12
Gviz1.22.0
HDF5Array1.6.0
HSMMSingleCell0.112.0
Hmisc4.0-3
IHW1.6.0
IRanges2.12.0
KEGG.db3.2.3
KMsurv0.1-5
Lahman6.0-0
LearnBayes2.15
MODA1.4.0
MatrixModels0.4-1
ModelMetrics1.1.0
MotIV1.34.0
MultiAssayExperiment1.4.4
NMF0.20.6
Nozzle.R11.1-1
OrganismDbi1.20.0
PKI0.1-5.1
ProtGenerics1.10.0
R.cache0.12.0
R.methodsS31.7.1
R.oo1.21.0
R.rsp0.41.0
R.utils2.6.0
R62.2.2
RANN2.5.1
RBGL1.54.0
RCircos1.2.0
RColorBrewer1.1-2
RCurl1.95-4.8
RJSONIO1.3-0
RMySQL0.10.13
RNeXML2.0.8
ROC1.54.0
RSQLite2.0
RSpectra0.12-0
RTCGAToolbox2.8.0
RUnit0.4.31
RaggedExperiment1.2.3
Rcpp0.12.14
RcppArmadillo0.8.100.1.0
RcppCCTZ0.2.3
RcppEigen0.3.3.3.1
RcppGSL0.3.3
RcppParallel4.3.20
RcppRoll0.2.2
Rgraphviz2.22.0
Rhdf5lib1.0.0
Rhtslib1.10.0
Rsamtools1.30.0
Rtsne0.13
S4Vectors0.16.0
SQUAREM2017.10-1
ShortRead1.36.0
SingleCellExperiment1.0.0
SparseM1.77
StanHeaders2.16.0-1
SummarizedExperiment1.8.0
TCC1.18.0
TH.data1.0-8
TSP1.1-5
TTR0.23-2
TxDb.Celegans.UCSC.ce6.ensGene3.2.2
TxDb.Dmelanogaster.UCSC.dm3.ensGene3.2.2
TxDb.Hsapiens.UCSC.hg18.knownGene3.2.2
TxDb.Hsapiens.UCSC.hg19.knownGene3.2.2
TxDb.Hsapiens.UCSC.hg38.knownGene3.4.0
TxDb.Mmusculus.UCSC.mm10.knownGene3.4.0
TxDb.Mmusculus.UCSC.mm9.knownGene3.2.2
TxDb.Rnorvegicus.UCSC.rn4.ensGene3.2.2
UpSetR1.3.3
VGAM1.0-4
VIM4.7.0
VariantAnnotation1.24.2
VennDiagram1.6.18
WGCNA1.61
WikidataR1.4.0
WikipediR1.5.0
XML3.98-1.9
XVector0.18.0
abind1.4-5
acepack1.4.1
ade41.7-8
ade4TkGUI0.2-9
adegenet2.1.0
adegraphics1.0-8
adephylo1.1-10
affy1.56.0
affyio1.48.0
airway0.112.0
akima0.6-2
alr41.0.5
amap0.8-14
annotate1.56.1
ape5.0
apeglm1.0.1
aroma.light3.8.0
ashr2.0.5
assertthat0.2.0
backports1.1.1
base642.0
base64enc0.1-3
baySeq2.12.0
bayesplot1.4.0
bbmle1.0.20
bdsmatrix1.3-2
beachmat1.0.2
beeswarm0.2.3
bindr0.1
bindrcpp0.2
biocViews1.46.0
biomaRt2.34.0
biomformat1.6.0
biovizBase1.26.0
bit1.1-12
bit640.9-7
bitops1.0-6
bladderbatch1.16.0
blob1.1.0
bold0.5.0
bookdown0.5
brew1.0-6
brglm0.6.1
broom0.4.3
caTools1.17.1
car2.1-6
carData3.0-0
caret6.0-77
checkmate1.8.5
chipseq1.28.0
chron2.3-51
circlize0.4.2
circular0.4-93
cmprsk2.2-7
coda0.19-1
colorspace1.3-2
colourpicker1.0
combinat0.0-8
commonmark1.4
corpcor1.6.9
corrplot0.84
covr3.0.1
cowplot0.9.1
crayon1.3.4
crosstalk1.0.0
crul0.4.0
csaw1.12.0
curl3.0
cvTools0.3.2
d3heatmap0.6.1.1
dada21.6.0
data.table1.10.4-3
dbplyr1.1.0
ddalpha1.3.1
deSolve1.20
debugme1.1.0
deldir0.1-14
dendextend1.6.0
densityClust0.3
desc1.1.1
destiny2.6.1
devtools1.13.4
dichromat2.0-0
digest0.6.12
dimRed0.1.0
diptest0.75-7
doParallel1.0.11
dotCall640.9-04
dplyr0.7.4
dtplyr0.0.2
dygraphs1.1.1.4
dynamicTreeCut1.63-1
e10711.6-8
ecodist2.0.1
edgeR3.20.1
effects4.0-0
ellipse0.3-8
emdbook1.3.9
emojifont0.5.1
ensembldb2.2.0
estimability1.2
etrunct0.1
evaluate0.10.1
exactRankTests0.8-29
expm0.999-2
expsmooth2.3
fastICA1.2-1
fastcluster1.1.24
fastmatch1.1-0
fdrtool1.2.15
fit.models0.5-14
flexmix2.3-14
foreach1.4.3
forecast8.2
fpc2.1-10
fracdiff1.4-2
fts0.9.9
futile.logger1.4.3
futile.options1.0.0
gam1.14-4
gapminder0.3.0
gclus1.3.1
gdata2.18.0
gdtools0.1.6
gee4.13-19
geiger2.0.6
geneLenDataBase1.14.0
genefilter1.60.0
geneplotter1.56.0
getopt1.20.1
ggbeeswarm0.6.0
ggplot22.2.1
ggplot2movies0.0.1
ggpubr0.1.6
ggrepel0.7.0
ggsci2.8
ggsignif0.4.0
ggtree1.10.0
git2r0.19.0
glmnet2.0-13
glue1.2.0
gmailr0.7.1
gmodels2.16.2
googleVis0.6.2
goseq1.30.0
gower0.1.2
gplots3.0.1
grImport0.9-0
graph1.56.0
gridBase0.4-7
gridExtra2.3
gtable0.2.0
gtools3.5.0
heatmaply0.13.0
hexbin1.27.1
hflights0.1
hgu95av2.db3.2.3
hierfstat0.04-22
highr0.6
hms0.4.0
hom.Hs.inp.db3.1.2
htSeqTools1.26.0
htmlTable1.11.0
htmltools0.3.6
htmlwidgets0.9
httpcode0.2.0
httpuv1.3.5
httr1.3.1
hunspell2.7
hwriter1.3.2
ibdreg0.2.5
idr1.2
igraph1.1.2
igraph00.5.7
igraphdata1.0.1
illuminaio0.20.0
impute1.52.0
inline0.3.14
interactiveDisplayBase1.16.0
ipred0.9-6
irlba2.3.1
iterators1.0.8
itertools0.1-3
jose0.1
jpeg0.1-8
jsonlite1.5
kernlab0.9-25
km.ci0.5-2
knitr1.17
labeling0.3
laeken0.4.6
lambda.r1.2
latticeExtra0.6-28
lava1.5.1
lazyeval0.2.1
leaps3.0
limSolve1.5.5.3
limma3.34.3
lintr1.0.2
lme41.1-14
lmerTest2.0-36
lmtest0.9-35
locfit1.5-9.1
loo1.1.0
lpSolve5.6.13
lpsymphony1.6.0
lsmeans2.27-61
lubridate1.7.1
magrittr1.5
mapdata2.2-6
mapproj1.2-5
maps3.2.0
maptools0.9-2
markdown0.8
matrixStats0.52.2
maxLik1.3-4
maxstat0.7-25
mclust5.4
memoise1.1.0
memuse4.0-0
metagenomeSeq1.20.0
microbenchmark1.4-2.1
mime0.5
miniUI0.1.1
minqa1.2.4
miscTools0.6-22
mixOmics6.3.1
mnormt1.5-5
modeltools0.2-21
mondate0.10.01.02
monocle2.6.1
motifStack1.22.0
multcomp1.4-8
multtest2.34.0
munsell0.4.3
mvoutlier2.0.8
mvtnorm1.0-6
nanotime0.2.0
natserv0.1.4
naturalsort0.1.3
ncbit2013.03.29
nloptr1.0.4
numDeriv2016.8-1
nycflights130.2.2
openssl0.9.9
optparse1.4.4
org.At.tair.db3.5.0
org.Ce.eg.db3.5.0
org.Hs.eg.db3.5.0
org.Mm.eg.db3.5.0
org.Sc.sgd.db3.5.0
packrat0.4.8-1
pamr1.55
parathyroidSE1.16.0
pasilla1.6.0
pbapply1.3-3
pbkrtest0.4-7
pca3d0.10
pcaPP1.9-72
pegas0.10
permute0.9-4
phangorn2.3.1
pheatmap1.0.8
phylobase0.8.4
phyloseq1.22.3
picante1.6-2
pinfsc501.1.0
pinp0.0.4
pixmap0.4-11
pkgKitten0.1.4
pkgconfig2.0.1
pkgmaker0.22
plm1.6-6
plogr0.1-1
plotly4.7.1
plotrix3.6-6
plotwidgets0.4
pls2.6-0
plyr1.8.4
png0.1-7
poppr2.5.0
prabclus2.2-6
pracma2.1.1
praise1.0.0
preprocessCore1.40.0
prettydoc0.2.0
prettyunits1.0.2
processx2.0.0.1
prodlim1.6.1
profdpm3.3
profileModel0.5-9
progress1.1.2
proto1.0.0
proxy0.4-19
pscl1.5.2
psych1.7.8
purrr0.2.4
pvclust2.0-0
qap0.1-1
qlcMatrix0.9.5
quadprog1.5-5
quantmod0.4-11
quantreg5.34
rARPACK0.11-0
rGADEM2.26.0
randomForest4.6-12
rbenchmark1.0.0
reactome.db1.62.0
readr1.1.1
recipes0.1.1
regioneR1.10.0
registry0.5
rentrez1.1.0
reshape0.8.7
reshape21.4.2
rex1.1.2
rgl0.98.1
rhdf52.22.0
ritis0.7.0
rjson0.2.15
rlang0.1.4
rmarkdown1.8
rncl0.8.2
rngtools1.2.4
robCompositions2.0.6
robust0.4-18
robustbase0.92-8
rotl3.0.3
roxygen26.0.1
rprojroot1.2
rrcov1.4-3
rredlist0.4.0
rsconnect0.8.5
rstan2.16.2
rstantools1.3.0
rstudioapi0.7
rticles0.4.1
rtracklayer1.38.1
rvcheck0.0.9
rversions1.0.3
sROC0.1-2
samr2.0
sandwich2.4-0
scales0.5.0
scater1.6.1
scatterplot3d0.3-40
scran1.6.5
segmented0.5-3.0
sendmailR1.2-1
seqLogo1.44.0
seqinr3.4-5
seriation1.2-2
sfsmisc1.1-1
sgeostat1.0-27
shape1.4.3
shiny1.0.5
shinydashboard0.6.1
shinyjs0.9.1
shinythemes1.1.1
showtext0.5
showtextdb2.0
slam0.1-40
smoother1.1
snow0.4-2
solrium1.0.0
sourcetools0.1.6
sp1.2-5
spData0.2.6.7
spam2.1-1
spdep0.7-4
sphet1.6
splancs2.01-40
splm1.4-10
statmod1.4.30
stringdist0.9.4.6
stringi1.1.6
stringr1.2.0
strucchange1.5-1
subplex1.4-1
survMisc0.5.4
survey3.32-1
survminer0.4.1
sva3.26.0
svglite1.2.1
sysfonts0.7.1
systemPipeR1.12.0
tagcloud0.6
taxize0.9.0
testthat1.0.2
threejs0.3.1
tibble1.3.4
tidyr0.7.2
tidyselect0.2.3
tiff0.1-5
timeDate3042.101
timeSeries3042.102
tis1.32
tkrplot0.0-23
tmod0.31
trackViewer1.14.0
treeio1.2.1
triebeard0.3.0
trimcluster0.1-2
tripack1.3-8
truncnorm1.0-7
tseries0.10-42
tufte0.2
tximport1.6.0
tximportData1.6.0
urltools1.6.0
uuid0.1-2
vcd1.4-3
vcfR1.5.0
vegan2.4-5
vipor0.4.5
viridis0.4.0
viridisLite0.2.0
vsn3.46.0
waveslim1.7.5
webshot0.5.0
webutils0.6
whisker0.3-2
wikitaxa0.1.4
withr2.1.0
worrms0.2.0
xml21.1.1
xtable1.8-2
xts0.10-0
yaml2.1.15
zebrafishRNASeq0.112.0
zipcode1.0
zlibbioc1.24.0
zoo1.8-0

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