R

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

Seminar Slides

Programming (A. Pacheco, J. Mack)
Visualization (A. Pacheco, J. Mack)

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

R 3.3.3

module load r-project/3.3.3

R 3.4.2

module load r-project/3.4.2

R 3.4.3

module load anaconda/python3

R 3.5.3

module load r-project/3.5.3

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

mkdir -p ${R_LIBS}

Start interactive R session and install package using the command

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

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