Uppsala Multidisciplinary Center for Advanced Computational Science

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).

PackageVersion
AMOUNTAIN1.2.0
ASCAT2.4.4
AnnotationDbi1.38.2
AnnotationFilter1.0.0
AnnotationForge1.18.2
AnnotationHub2.8.3
BBmisc1.11
BH1.65.0-1
BSgenome1.44.2
BatchJobs1.6
BiasedUrn1.07
Biobase2.36.2
BiocGenerics0.22.1
BiocInstaller1.26.1
BiocParallel1.10.1
Biostrings2.44.2
Category2.42.1
ChIPQC1.12.3
ChIPpeakAnno3.10.2
DBI0.7
DESeq1.28.0
DESeq21.16.1
DEXSeq1.22.0
DEoptimR1.0-8
DT0.2
DelayedArray0.2.7
DiffBind2.4.8
FNN1.1
Formula1.2-2
GO.db3.4.1
GOstats2.42.0
GSEABase1.38.2
GenomeInfoDb1.12.3
GenomeInfoDbData0.99.0
GenomicAlignments1.12.2
GenomicFeatures1.28.5
GenomicRanges1.28.6
Glimma1.4.0
Gviz1.20.0
Hmisc4.0-3
IRanges2.10.5
Lahman6.0-0
LearnBayes2.15
MODA1.2.0
MultiAssayExperiment1.2.1
NMF0.20.6
Nozzle.R11.1-1
ProtGenerics1.8.0
R62.2.2
RBGL1.52.0
RColorBrewer1.1-2
RCurl1.95-4.8
RJSONIO1.3-0
ROC1.52.0
RSQLite2.0
RSpectra0.12-0
Rcpp0.12.13
RcppArmadillo0.8.100.1.0
RcppEigen0.3.3.3.0
RcppParallel4.3.20
Rhtslib1.8.0
Rsamtools1.28.0
S4Vectors0.14.7
ShortRead1.34.2
SummarizedExperiment1.6.5
TCC1.16.0
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
VariantAnnotation1.22.3
VennDiagram1.6.17
WGCNA1.61
XML3.98-1.9
XVector0.16.0
abind1.4-5
acepack1.4.1
ade41.7-8
adegenet2.1.0
akima0.6-2
amap0.8-14
annotate1.54.0
ape4.1
assertthat0.2.0
backports1.1.1
base64enc0.1-3
baySeq2.10.0
beeswarm0.2.3
bindr0.1
bindrcpp0.2
biomaRt2.32.1
biomformat1.4.0
biovizBase1.24.0
bit1.1-12
bit640.9-7
bitops1.0-6
blob1.1.0
brew1.0-6
caTools1.17.1
checkmate1.8.5
chipseq1.26.1
chron2.3-51
coda0.19-1
colorspace1.3-2
combinat0.0-8
corpcor1.6.9
crayon1.3.4
csaw1.10.0
curl3.0
dada21.4.0
data.table1.10.4-3
deSolve1.20
deldir0.1-14
dendextend1.5.2
dichromat2.0-0
digest0.6.12
diptest0.75-7
doParallel1.0.11
dplyr0.7.4
dynamicTreeCut1.63-1
ecodist2.0.1
edgeR3.18.1
ellipse0.3-8
ensembldb2.0.4
evaluate0.10.1
expm0.999-2
fail1.3
fastcluster1.1.24
fit.models0.5-14
flexmix2.3-14
foreach1.4.3
fpc2.1-10
futile.logger1.4.3
futile.options1.0.0
gdata2.18.0
gee4.13-19
geiger2.0.6
geneLenDataBase1.12.0
genefilter1.58.1
geneplotter1.54.0
getopt1.20.0
ggbeeswarm0.6.0
ggplot22.2.1
ggrepel0.7.0
ggtree1.8.2
glue1.2.0
gmodels2.16.2
goseq1.28.0
gplots3.0.1
graph1.54.0
gridBase0.4-7
gridExtra2.3
gtable0.2.0
gtools3.5.0
hexbin1.27.1
hflights0.1
highr0.6
htSeqTools1.24.0
htmlTable1.9
htmltools0.3.6
htmlwidgets0.9
httpuv1.3.5
httr1.3.1
hwriter1.3.2
idr1.2
igraph1.1.2
igraph00.5.7
impute1.50.1
interactiveDisplayBase1.14.0
irlba2.3.1
iterators1.0.8
jsonlite1.5
kernlab0.9-25
knitr1.17
labeling0.3
lambda.r1.2
latticeExtra0.6-28
lazyeval0.2.1
limma3.32.10
lme41.1-14
lmerTest2.0-33
locfit1.5-9.1
magrittr1.5
maps3.2.0
markdown0.8
matrixStats0.52.2
mclust5.3
memoise1.1.0
memuse3.0-1
microbenchmark1.4-2.1
mime0.5
minqa1.2.4
mixOmics6.3.0
modeltools0.2-21
multtest2.32.0
munsell0.4.3
mvtnorm1.0-6
naturalsort0.1.3
ncbit2013.03.29
nloptr1.0.4
openssl0.9.7
optparse1.4.4
org.Mm.eg.db3.4.1
pca3d0.10
pcaPP1.9-72
permute0.9-4
pheatmap1.0.8
phyloseq1.20.0
picante1.6-2
pinfsc501.1.0
pkgconfig2.0.1
pkgmaker0.22
plogr0.1-1
plotrix3.6-6
plotwidgets0.4
plyr1.8.4
prabclus2.2-6
praise1.0.0
preprocessCore1.38.1
proto1.0.0
purrr0.2.4
pvclust2.0-0
rARPACK0.11-0
reactome.db1.59.1
regioneR1.8.1
registry0.3
reshape0.8.7
reshape21.4.2
rgl0.98.1
rhdf52.20.0
rjson0.2.15
rlang0.1.2
rmarkdown1.6
rngtools1.2.4
robust0.4-18
robustbase0.92-7
rprojroot1.2
rrcov1.4-3
rtracklayer1.36.6
rvcheck0.0.9
samr2.0
scales0.5.0
scater1.4.0
scran1.4.5
segmented0.5-2.2
sendmailR1.2-1
seqinr3.4-5
shiny1.0.5
shinydashboard0.6.1
snow0.4-2
snpStats1.26.0
sourcetools0.1.6
sp1.2-5
spdep0.6-15
statmod1.4.30
stringi1.1.5
stringr1.2.0
subplex1.4-1
sva3.24.4
systemPipeR1.10.2
tagcloud0.6
testthat1.0.2
tibble1.3.4
tidyr0.7.2
tidyselect0.2.2
tkrplot0.0-23
tmod0.31
treeio1.0.2
trimcluster0.1-2
tximport1.4.0
vcfR1.5.0
vegan2.4-4
vipor0.4.5
viridis0.4.0
viridisLite0.2.0
whisker0.3-2
xtable1.8-2
yaml2.1.14
zlibbioc1.22.0
zoo1.8-0

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