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R is a free software environment for statistical computing and graphics.

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A comprehensive list of packages is available in the RStudio singularity images. Click here to view the list and instructions for using them outside RStudio.

How to install R packages?

A variety of R packages are installed however it is recommended that users install packages (newer and updated versions) in their own home directory.

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title	Deprecated CentOS 7.x Software: Use module load cent7 to use the following modules

Which versions of R are available?

There are four version of R available, 3.3.3, 3.4.2, 3.4.3 and 3.5.3. Of the two 3.5.3 version, one version labelled r-bio contains packages from Bioconductor for Bioinformatics research.

Usage

Code Block

language	bash
title	R 3.3.3

module load r-project/3.3.3

Code Block

language	bash
title	R 3.4.2

module load r-project/3.4.2

Code Block

language	bash
title	R 3.4.3

module load anaconda/python3

Code Block

language	bash
title	R 3.5.3

module load r-project/3.5.3

Code Block

language	bash
title	r 3.5.3 for Bioinformatics

module load r-bio/3.5.3

How to install R packages?

A variety of R packages are installed however it is recommended that users install packages (newer and updated versions) in their own home directory.

The r-project/3.x.y modules sets up a variable, R_LIBS, to install packages in your home directory. Make sure the R_LIBS directory exists

Code Block

language	bash

mkdir -p ${R_LIBS}

Start interactive R session and install package using the command

Code Block

language	bash

install.packages('packagename')

Alternatively, you can add install.packages('packagename') within your R script

If you get an error installing packages locally, then use the command

Code Block

language	bash

install.packages('packagename',lib=Sys.getenv("R_LIBS"))

Installed Packages

Package	3.3.3	3.4.2	3.4.3	3.5.3	r-bio
abind	1.4-5	1.4-5			1.4-3
acepack					1.4.1
amap					0.8-16
annotate					1.58.0
AnnotationDbi					1.42.1
ape					5.3
argparse					1.1.1
askpass	1.1	1.1		1.1
assertthat	0.2.0	0.2.0	0.2.0	0.2.0	0.2.0
backports	1.1.2	1.1.1	1.1.2	1.1.3	1.1.1
base	3.3.3	3.4.2	3.4.3	3.5.3	3.5.3
base64enc	0.1-3	0.1-3	0.1-3	0.1-3	0.1-3
BH	1.65.0-1	1.65.0-1	1.65.0-1	1.69.0-1	1.69.0-1
BiasedUrn					1.07
bindr	0.1	0.1	0.1		0.1.1
bindrcpp	0.2	0.2	0.2		0.2.2
Biobase					2.40.0
BiocGenerics					0.26.0
BiocParallel					1.14.2
biomaRt					2.36.1
Biostrings					2.48.0
bit					1.1-12
bit64					0.9-7
bitops	1.0-6	1.0-6	1.0-6		1.0-6
blob					1.1.0
boot	1.3-18	1.3-20	1.3-20	1.3-20	1.3-20
broom	0.4.3	0.4.3	0.4.3	0.5.1
callr	3.2.0	2.0.1	1.0.0	3.1.1	3.0.0
car			2.1-6
caret			6.0-78
caTools	1.17.1.2	1.17.1	1.17.1		1.17.1
cellranger	1.1.0	1.1.0	1.1.0	1.1.0	1.1.0
checkmate					1.8.4
chron			2.3-51
class	7.3-14	7.3-14	7.3-14	7.3-15	7.3-15
cli	1.0.0	1.0.0	1.0.0	1.0.1	1.0.1
clipr	0.4.0	0.5.0	0.4.0	0.5.0	0.4.0
clisymbols	1.2.0	1.2.0		1.2.0
cluster	2.0.5	2.0.6	2.0.6	2.0.7-1	2.0.7-1
codetools	0.2-15	0.2-15	0.2-15	0.2-16	0.2-16
colorspace	1.3-2	1.3-2	1.3-2	1.4-0	1.3-2
compiler	3.3.3	3.4.2	3.4.3	3.5.3	3.5.3
covr					3.0.1
crayon	1.3.4	1.3.4	1.3.4	1.3.4	1.3.4
ctc					1.54.0
curl	3.1	3.1	3.1	3.3	3.3
CVST			0.2-1
datasets	3.3.3	3.4.2	3.4.3	3.5.3	3.5.3
data.table			1.10.4-3		1.11.8
DBI	0.7	0.7	0.7	1.0.0	0.7
dbplyr	1.2.0	1.2.0	1.1.0	1.3.0	1.2.2
ddalpha			1.3.1
debugme	1.1.0	1.1.0
DelayedArray					0.6.5
DEoptimR			1.0-8
desc	1.2.0	1.2.0		1.2.0
devtools	2.0.1			2.0.1	1.12.0
dichromat	2.0-0	2.0-0	2.0-0		2.0-0
digest	0.6.14	0.6.12	0.6.13	0.6.18	0.6.12
dimRed			0.1.0
dplyr	0.7.4	0.7.4	0.7.4	0.8.0.1	0.7.7
DRR			0.0.2
dygraphs	1.1.1.6	1.1.1.4
ellipsis	0.1.0	0.1.0		0.1.0
evaluate	0.10.1	0.10.1	0.10.1	0.13	0.10.1
fansi	0.4.0	0.4.0		0.4.0	1.1.25
fftwtools					0.9-8
findpython					1.0.3
flexdashboard	0.5.1.1	0.5.1
forcats	0.2.0	0.2.0	0.2.0	0.4.0	0.2.0
foreach			1.4.4
foreign	0.8-67	0.8-69	0.8-69	0.8-71	0.8-71
formatR			1.5
fs	1.2.6	1.2.7		1.2.6
genefilter					1.62.0
GenomeInfoDb					1.16.0
GenomeInfoDbData					1.1.0
GenomicRanges					1.32.6
generics	0.0.2	0.0.2		0.0.2
ggplot2	2.2.1	2.2.1	2.2.1	3.1.0	3.2.0
gh	1.0.1	1.0.1		1.0.1
git2r	0.24.0	0.25.2		0.24.0	0.18.0
glmnet			2.0-13
glue	1.2.0	1.2.0	1.2.0	1.3.1	1.2.0
gower			0.1.2
graphics	3.3.3	3.4.2	3.4.3	3.5.3	3.5.3
grDevices	3.3.3	3.4.2	3.4.3	3.5.3	3.5.3
grid	3.3.3	3.4.2	3.4.3	3.5.3	3.5.3
gtable	0.2.0	0.2.0	0.2.0	0.2.0	0.2.0
gtools	3.8.1	3.5.0			3.5.0
haven	1.1.1	1.1.1	1.1.0	2.1.0	1.1.0
hexbin			1.27.1
highr	0.6	0.6	0.6	0.7	0.6
hms	0.4.0	0.4.1	0.4.0	0.4.2	0.3
htmltools	0.3.6	0.3.6	0.3.6	0.3.6	0.3.6
htmlwidgets	1.3	0.9	0.9		0.9
httpuv	1.5.1	1.3.5	1.3.5		1.3.5
httr	1.3.1	1.3.1	1.3.1	1.4.0	1.3.1
ini	0.3.1	0.3.1		0.3.1
ipred			0.9-6
IRdisplay			0.4.4
IRkernel			0.8.11
iterators			1.0.9
jsonlite	1.5	1.5	1.5	1.6	1.5
kernlab			0.9-25
KernSmooth	2.23-15	2.23-15	2.23-15	2.23-15	2.23-15
knitr	1.18	1.19	1.18	1.22
labeling	0.3	0.3	0.3	0.3	0.3
later	0.8.0
lattice	0.20-34	0.20-35	0.20-35	0.20-38	0.20-38
lava			1.5.1
lazyeval	0.2.1	0.2.0	0.2.1	0.2.1	0.2.0
lme4			1.1-15
lubridate	1.7.1	1.7.2	1.7.1	1.7.4	1.7.1
magrittr	1.5	1.5	1.5	1.5	1.5
maps			3.2.0
markdown	0.8	0.8	0.8	0.9	0.8
MASS	7.3-45	7.3-47	7.3-48	7.3-51.1	7.3-51.1
Matrix	1.2-8	1.2-11	1.2-12	1.2-15	1.2-15
MatrixModels			0.4-1		0.52.2
matrixStats	0.54.0	0.53.1
memoise	1.1.0	1.1.0		1.1.0	1.1.0
methods	3.3.3	3.4.2	3.4.3	3.5.3	3.5.3
mgcv	1.8-17	1.8-20	1.8-22	1.8-27	1.8-27
mime	0.5	0.5	0.5	0.6	0.5
minqa			1.2.4
mnormt	1.5-5	1.5-5	1.5-5		1.5-5
ModelMetrics			1.1.0
modelr	0.1.1	0.1.1	0.1.1	0.1.4
munsell	0.4.3	0.4.3	0.4.3	0.5.0	0.4.3
nlme	3.1-131	3.1-131	3.1-131	3.1-137	3.1-137
nloptr			1.0.4
nnet	7.3-12	7.3-12	7.3-12	7.3-12	7.3-12
numDeriv			2016.8-1
openssl	0.9.9	0.9.9	0.9.9	1.2.2	0.9.7
optparse					1.6.0
padr	0.4.1	0.4.0
parallel	3.3.3	3.4.2	3.4.3	3.5.3	3.5.3
pbdZMQ			0.3-0
pbkrtest			0.4-7
phangorn					2.5.5
pillar	1.1.0	1.1.0	1.0.1	1.3.1	1.3.1
pkgbuild	1.0.2	1.0.3		1.0.2
pkgconfig	2.0.1	2.0.1	2.0.1	2.0.2	2.0.2
pkgload	1.0.2	1.0.2		1.0.2
plogr	0.1-1	0.1-1	0.1-1	0.2.0	0.2.0
plot3D					1.1.1
plyr	1.8.4	1.8.4	1.8.4	1.8.4	1.8.4
png	0.1-7	0.1-7
pracma	2.2.5	2.1.4
praise	1.0.0	1.0.0			1.0.0
prettyunits	1.0.2	1.0.2		1.0.2	1.0.2
processx	3.3.0	3.3.0		3.3.0	3.2.0
prodlim			1.6.1
progress	1.2.0	1.2.0		1.2.0	1.1.2
promises	1.0.1
proto			1.0.0		1.0.0
ps	1.3.0	1.3.0		1.3.0	1.1.0
psych	1.7.8	1.7.8	1.7.8
purrr	0.2.4	0.2.4	0.2.4	0.3.1	0.2.4
quantmod			0.4-12
quantreg			5.34
R6	2.2.2	2.2.2	2.2.2	2.4.0	2.2.2
randomForest			4.6-12
rbokeh			0.6.3
rcmdcheck	1.3.2	1.3.2		1.3.2
RColorBrewer	1.1-2	1.1-2	1.1-2	1.1-2
Rcpp	0.12.15	0.12.13	0.12.14	1.0.0	1.0.0
RcppArmadillo					0.8.100.1.0
RcppEigen			0.3.3.3.1
RcppRoll			0.2.2
RCurl					1.95-4.8
readr	1.1.1	1.1.1	1.1.1	1.3.1	1.1.1
readxl	1.0.0	1.0.0	1.0.0	1.3.1	1.1.0
recipes			0.1.1
rematch	1.0.1	1.0.1	1.0.1	1.0.1	1.0.1
remotes	2.0.2	2.0.4		2.0.2
repr			0.12.0
reprex	0.1.1	0.1.2	0.1.1	0.2.1
reshape2	1.4.3	1.4.2	1.4.3	1.4.3	1.4.2
RJSONIO			1.3-0
rlang	0.1.6	0.1.6	0.1.6	0.3.1	0.3.1
rmarkdown	1.8	1.6	1.8	1.12
R.matlab	3.6.2	3.6.1
R.methodsS3	1.7.1	1.7.1
Rmpi					0.6-6
robustbase			0.92-8
R.oo	1.22.0	1.21.0
rpart	4.1-10	4.1-11	4.1-11	4.1-13	4.1-13
rprojroot	1.3-2	1.2	1.3-1	1.3-2	1.2
Rsamtools					1.32.2
RSQLite					2.0
rstudioapi	0.7	0.7	0.7	0.9.0	0.7
R.utils	2.8.0	2.5.0
rvest	0.3.2	0.3.2	0.3.2	0.3.2	0.3.2
rzmq			0.9.3
S4Vectors					0.18.3
scales	0.5.0	0.5.0	0.5.0	1.0.0	0.5.0
selectr	0.3-1	0.3-1	0.3-1	0.4-1	0.3-1
sessioninfo	1.1.1	1.1.1		1.1.1
sfsmisc			1.1-1
shiny	1.3.0	1.0.5	1.0.5		1.0.5
snow					0.4-2
sourcetools	0.1.7	0.1.6	0.1.6		0.1.6
SparseM			1.77
spatial	7.3-11	7.3-11	7.3-11	7.3-11	7.3-11
splines	3.3.3	3.4.2	3.4.3	3.5.3	3.5.3
stats	3.3.3	3.4.2	3.4.3	3.5.3	3.5.3
stats4	3.3.3	3.4.2	3.4.3	3.5.3	3.5.3
stringi	1.1.6	1.1.5	1.1.6	1.4.3	1.1.5
stringr	1.2.0	1.2.0	1.2.0	1.4.0	1.2.0
survival	2.40-1	2.41-3	2.41-3	2.43-3	2.43-3
sys	3.1	3.1		3.1
tcltk	3.3.3	3.4.2	3.4.3	3.5.3	3.5.3
testthat	2.0.1	2.0.0			1.0.2
tibble	1.4.1	1.4.2	1.4.1	2.0.1	2.0.1
tidyr	0.7.2	0.8.0	0.7.2	0.8.3	0.7.2
tidyselect	0.2.3	0.2.3	0.2.3	0.2.5	0.2.3
tidyverse	1.2.1	1.2.1	1.2.1	1.2.1
timeDate			3042.101
tinytex	0.11	0.11		0.11
tools	3.3.3	3.4.2	3.4.3	3.5.3	3.5.3
TTR			0.23-2
usethis	1.4.0			1.4.0
utf8	1.1.3	1.1.3	1.1.2	1.1.4	1.1.3
utils	3.3.3	3.4.2	3.4.3	3.5.3	3.5.3
uuid			0.1-2
viridisLite	0.2.0	0.2.0	0.2.0	0.3.0	0.2.0
whisker	0.3-2	0.3-2	0.3-2	0.3-2	0.3-2
withr	2.1.2	2.1.2	2.1.1	2.1.2	2.1.2
xfun	0.6	0.6		0.5
XML					3.98-1.9
xml2	1.1.1	1.2.0	1.1.1	1.2.0	1.1.1
xopen	1.0.0	1.0.0		1.0.0
xtable	1.8-3	1.8-2	1.8-2		1.8-2
xts	0.11-2	0.10-1	0.10-1
XVector					0.20.0
yaml	2.1.16	2.1.14	2.1.16	2.2.0	2.1.14
zlibbioc					1.26.0
zoo	1.8-5	1.8-0	1.8-0

Image Added

Versions Compared

Old Version 22

New Version 23

Key

Which versions of R are available?

Usage

How to install R packages?

Installed Packages