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).

Package Version
acepack 1.4.1
ade4 1.7-6
adegenet 2.0.1
akima 0.6-2
AMOUNTAIN 1.2.0
annotate 1.54.0
AnnotationDbi 1.38.1
AnnotationFilter 1.0.0
AnnotationHub 2.8.1
ape 4.1
ASCAT 2.4.4
assertthat 0.2.0
backports 1.1.0
base64enc 0.1-3
beeswarm 0.2.3
BH 1.62.0-1
BiasedUrn 1.07
Biobase 2.36.2
BiocGenerics 0.22.0
BiocInstaller 1.26.0
BiocParallel 1.10.1
biomaRt 2.32.0
Biostrings 2.44.1
biovizBase 1.24.0
bitops 1.0-6
BSgenome 1.44.0
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 2.6
dada2 1.4.0
data.table 1.10.4
DBI 0.6-1
DelayedArray 0.2.7
deldir 0.1-14
dendextend 1.5.2
DEoptimR 1.0-8
DESeq 1.28.0
DESeq2 1.16.1
deSolve 1.14
DEXSeq 1.22.0
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 3.18.1
ellipse 0.3-8
ensembldb 2.0.3
evaluate 0.10
expm 0.999-2
fastcluster 1.1.22
flexmix 2.3-14
foreach 1.4.3
Formula 1.2-1
fpc 2.1-10
futile.logger 1.4.3
futile.options 1.0.0
gdata 2.17.0
geiger 2.0.6
genefilter 1.58.1
geneLenDataBase 1.12.0
geneplotter 1.54.0
GenomeInfoDb 1.12.1
GenomeInfoDbData 0.99.0
GenomicAlignments 1.12.1
GenomicFeatures 1.28.2
GenomicRanges 1.28.3
getopt 1.20.0
ggplot2 2.2.1
ggtree 1.8.1
gmodels 2.16.2
GO.db 3.4.1
goseq 1.28.0
gplots 3.0.1
gridBase 0.4-7
gridExtra 2.2.1
gtable 0.2.0
gtools 3.5.0
Gviz 1.20.0
hexbin 1.27.1
highr 0.6
Hmisc 4.0-3
htmlTable 1.9
htmltools 0.3.6
htmlwidgets 0.8
httpuv 1.3.3
httr 1.2.1
hwriter 1.3.2
igraph 1.0.1
impute 1.50.1
interactiveDisplayBase 1.14.0
IRanges 2.10.2
irlba 2.2.1
iterators 1.0.8
jsonlite 1.5
kernlab 0.9-25
knitr 1.16
labeling 0.3
lambda.r 1.1.9
latticeExtra 0.6-28
lazyeval 0.2.0
LearnBayes 2.15
limma 3.32.2
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 5.3
memoise 1.1.0
microbenchmark 1.4-2.1
mime 0.5
minqa 1.2.4
MODA 1.2.0
modeltools 0.2-21
munsell 0.4.3
mvtnorm 1.0-6
naturalsort 0.1.3
ncbit 2013.03.29
nloptr 1.0.4
NMF 0.20.6
openssl 0.9.6
org.Mm.eg.db 3.4.1
pca3d 0.10
permute 0.9-4
picante 1.6-2
pkgmaker 0.22
plogr 0.1-1
plotrix 3.6-5
plotwidgets 0.4
plyr 1.8.4
prabclus 2.2-6
praise 1.0.0
preprocessCore 1.38.1
ProtGenerics 1.8.0
pvclust 2.0-0
R6 2.2.1
RColorBrewer 1.1-2
Rcpp 0.12.11
RcppArmadillo 0.7.800.2.0
RcppEigen 0.3.3.3.0
RcppParallel 4.3.20
RCurl 1.95-4.8
reactome.db 1.59.1
registry 0.3
reshape2 1.4.2
rgl 0.98.1
rlang 0.1.1
rmarkdown 1.5
rngtools 1.2.4
robustbase 0.92-7
rprojroot 1.2
Rsamtools 1.28.0
RSQLite 1.1-2
rtracklayer 1.36.3
rvcheck 0.0.8
S4Vectors 0.14.3
scales 0.4.1
segmented 0.5-2.0
seqinr 3.3-6
shiny 1.0.3
ShortRead 1.34.0
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
SummarizedExperiment 1.6.3
sva 3.24.0
tagcloud 0.6
testthat 1.0.2
tibble 1.3.3
tidyr 0.6.3
tkrplot 0.0-23
tmod 0.31
treeio 1.0.2
trimcluster 0.1-2
VariantAnnotation 1.22.1
vegan 2.4-3
VennDiagram 1.6.17
viridis 0.4.0
viridisLite 0.2.0
WGCNA 1.51
whisker 0.3-2
XML 3.98-1.7
xtable 1.8-2
XVector 0.16.0
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