Uppsala Multidisciplinary Center for Advanced Computational Science

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, within R, these should be available via library(package-name).

PackageVersion
ASCAT2.4.3
AnnotationDbi1.36.2
AnnotationHub2.6.4
BH1.62.0-1
BSgenome1.42.0
BiasedUrn1.07
Biobase2.34.0
BiocGenerics0.20.0
BiocInstaller1.24.0
BiocParallel1.8.1
Biostrings2.42.1
DBI0.5-1
DESeq1.26.0
DESeq21.14.1
DEXSeq1.20.1
DEoptimR1.0-8
Formula1.2-1
GO.db3.4.0
GenomeInfoDb1.10.2
GenomicAlignments1.10.0
GenomicFeatures1.26.2
GenomicRanges1.26.2
Gviz1.18.1
Hmisc4.0-2
IRanges2.8.1
LearnBayes2.15
NMF0.20.6
R62.2.0
RColorBrewer1.1-2
RCurl1.95-4.8
RSQLite1.1-2
Rcpp0.12.9
RcppArmadillo0.7.600.1.0
RcppEigen0.3.2.9.0
RcppParallel4.3.20
Rsamtools1.26.1
S4Vectors0.12.1
ShortRead1.32.0
SummarizedExperiment1.4.0
VariantAnnotation1.20.2
VennDiagram1.6.17
XML3.98-1.5
XVector0.14.0
acepack1.4.1
ade41.7-5
adegenet2.0.1
akima0.6-2
annotate1.52.1
ape4.0
assertthat0.1
backports1.0.5
base64enc0.1-3
biomaRt2.30.0
biovizBase1.22.0
bitops1.0-6
caTools1.17.1
checkmate1.8.2
chron2.3-49
coda0.19-1
colorspace1.3-2
combinat0.0-8
crayon1.3.2
curl2.3
dada21.2.1
data.table1.10.4
deSolve1.14
deldir0.1-12
dendextend1.4.0
dendextendRcpp0.6.1
dichromat2.0-0
digest0.6.12
diptest0.75-7
doParallel1.0.10
dplyr0.5.0
edgeR3.16.5
ensembldb1.6.2
evaluate0.10
flexmix2.3-13
foreach1.4.3
fpc2.1-10
futile.logger1.4.3
futile.options1.0.0
gdata2.17.0
geiger2.0.6
geneLenDataBase1.10.0
genefilter1.56.0
geneplotter1.52.0
getopt1.20.0
ggplot22.2.1
ggtree1.6.9
gmodels2.16.2
goseq1.26.0
gplots3.0.1
gridBase0.4-7
gridExtra2.2.1
gtable0.2.0
gtools3.5.0
hexbin1.27.1
highr0.6
htmlTable1.9
htmltools0.3.5
htmlwidgets0.8
httpuv1.3.3
httr1.2.1
hwriter1.3.2
igraph1.0.1
interactiveDisplayBase1.12.0
irlba2.1.2
iterators1.0.8
jsonlite1.2
kernlab0.9-25
knitr1.15.1
labeling0.3
lambda.r1.1.9
latticeExtra0.6-28
lazyeval0.2.0
limma3.30.9
lme41.1-12
lmerTest2.0-33
locfit1.5-9.1
magrittr1.5
maps3.1.1
markdown0.7.7
matrixStats0.51.0
mclust5.2.2
memoise1.0.0
microbenchmark1.4-2.1
mime0.5
minqa1.2.4
modeltools0.2-21
munsell0.4.3
mvtnorm1.0-5
naturalsort0.1.3
ncbit2013.03.29
nloptr1.0.4
openssl0.9.6
org.Mm.eg.db3.4.0
permute0.9-4
picante1.6-2
pkgmaker0.22
plogr0.1-1
plotrix3.6-4
plyr1.8.4
prabclus2.2-6
praise1.0.0
pvclust2.0-0
reactome.db1.58.0
registry0.3
reshape21.4.2
rmarkdown1.3
rngtools1.2.4
robustbase0.92-7
rprojroot1.2
rtracklayer1.34.1
scales0.4.1
segmented0.5-1.4
seqinr3.3-3
shiny1.0.0
snow0.4-2
sourcetools0.1.5
sp1.2-4
spdep0.6-9
statmod1.4.27
stringi1.1.2
stringr1.1.0
subplex1.2-2
sva3.22.0
testthat1.0.2
tibble1.2
tidyr0.6.1
tkrplot0.0-23
trimcluster0.1-2
vegan2.4-2
viridis0.3.4
whisker0.3-2
xtable1.8-2
yaml2.1.14
zlibbioc1.20.0
zoo1.7-14

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, 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
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
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
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
permute 0.9-4
picante 1.6-2
pkgmaker 0.22
plotrix 3.6-3
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
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
testthat 1.0.2
tibble 1.2
tidyr 0.6.0
tkrplot 0.0-23
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, 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
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
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
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
permute 0.9-4
picante 1.6-2
pkgmaker 0.22
plotrix 3.6-3
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
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
testthat 1.0.2
tibble 1.2
tidyr 0.6.0
tkrplot 0.0-23
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