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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.

...

Code Block

language	bash

install.packages('packagename')

Alternatively, you can add install.packages('packagename') within your R script. By default, R will try to install packages locally to ${HOME/x86_64-pc-linux-gnu-library. If you wish to use a different directory, then you need to set R_LIBS variable to point to that directory.

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

1.8-0

Code Block

language	bash

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

Expand

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

1.4-3

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

assertthat

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

base64enc

0.1-3

BH

1.65.0-1

1.69.0-1

BiasedUrn

1.07

bindr

0.1

0.1.1

bindrcpp

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

blob

1.1.0

boot

1.3-18

1.3-20

broom

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

cellranger

1.1.0

checkmate

1.8.4

chron

2.3-51

class

7.3-14

7.3-15

cli

1.0.0

1.0.1

clipr

0.4.0

0.5.0

0.4.0

0.5.0

0.4.0

clisymbols

1.2.0

cluster

2.0.5

2.0.6

2.0.7-1

codetools

0.2-15

0.2-16

colorspace

1.3-2

1.4-0

1.3-2

compiler

3.3.3

3.4.2

3.4.3

3.5.3

covr

3.0.1

crayon

1.3.4

ctc

1.54.0

curl

3.1

3.3

CVST

0.2-1

datasets

3.3.3

3.4.2

3.4.3

3.5.3

data.table

1.10.4-3

1.11.8

DBI

0.7

1.0.0

0.7

dbplyr

1.2.0

1.1.0

1.3.0

1.2.2

ddalpha

1.3.1

debugme

1.1.0

DelayedArray

0.6.5

DEoptimR

1.0-8

desc

1.2.0

devtools

2.0.1

1.12.0

dichromat

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

0.8.0.1

0.7.7

DRR

0.0.2

dygraphs

1.1.1.6

1.1.1.4

ellipsis

0.1.0

evaluate

0.10.1

0.13

0.10.1

fansi

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

0.4.0

0.2.0

foreach

1.4.4

foreign

0.8-67

0.8-69

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

ggplot2

2.2.1

3.1.0

3.2.0

gh

1.0.1

git2r

0.24.0

0.25.2

0.24.0

0.18.0

glmnet

2.0-13

glue

1.2.0

1.3.1

1.2.0

gower

0.1.2

graphics

3.3.3

3.4.2

3.4.3

3.5.3

grDevices

3.3.3

3.4.2

3.4.3

3.5.3

grid

3.3.3

3.4.2

3.4.3

3.5.3

gtable

0.2.0

gtools

3.8.1

3.5.0

haven

1.1.1

1.1.0

2.1.0

1.1.0

hexbin

1.27.1

highr

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

htmlwidgets

1.3

0.9

httpuv

1.5.1

1.3.5

httr

1.3.1

1.4.0

1.3.1

ini

0.3.1

ipred

0.9-6

IRdisplay

0.4.4

IRkernel

0.8.11

iterators

1.0.9

jsonlite

1.5

1.6

1.5

kernlab

0.9-25

KernSmooth

2.23-15

knitr

1.18

1.19

1.18

1.22

labeling

0.3

later

0.8.0

lattice

0.20-34

0.20-35

0.20-38

lava

1.5.1

lazyeval

0.2.1

0.2.0

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

maps

3.2.0

markdown

0.8

0.9

0.8

MASS

7.3-45

7.3-47

7.3-48

7.3-51.1

Matrix

1.2-8

1.2-11

1.2-12

1.2-15

MatrixModels

0.4-1

0.52.2

matrixStats

0.54.0

0.53.1

memoise

1.1.0

methods

3.3.3

3.4.2

3.4.3

3.5.3

mgcv

1.8-17

1.8-20

1.8-22

1.8-27

mime

0.5

0.6

0.5

minqa

1.2.4

mnormt

1.5-5

ModelMetrics

1.1.0

modelr

0.1.1

0.1.4

munsell

0.4.3

0.5.0

0.4.3

nlme

3.1-131

3.1-137

nloptr

1.0.4

nnet

7.3-12

numDeriv

2016.8-1

openssl

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

pbdZMQ

0.3-0

pbkrtest

0.4-7

phangorn

2.5.5

pillar

1.1.0

1.0.1

1.3.1

pkgbuild

1.0.2

1.0.3

1.0.2

pkgconfig

2.0.1

2.0.2

pkgload

1.0.2

plogr

0.1-1

0.2.0

plot3D

1.1.1

plyr

1.8.4

png

0.1-7

pracma

2.2.5

2.1.4

praise

1.0.0

prettyunits

1.0.2

processx

3.3.0

3.2.0

prodlim

1.6.1

progress

1.2.0

1.1.2

promises

1.0.1

proto

1.0.0

ps

1.3.0

1.1.0

psych

1.7.8

purrr

0.2.4

0.3.1

0.2.4

quantmod

0.4-12

quantreg

5.34

R6

2.2.2

2.4.0

2.2.2

randomForest

4.6-12

rbokeh

0.6.3

rcmdcheck

1.3.2

RColorBrewer

1.1-2

Rcpp

0.12.15

0.12.13

0.12.14

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

1.3.1

1.1.1

readxl

1.0.0

1.3.1

1.1.0

recipes

0.1.1

rematch

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

1.4.2

RJSONIO

1.3-0

rlang

0.1.6

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

Rmpi

0.6-6

robustbase

0.92-8

R.oo

1.22.0

1.21.0

rpart

4.1-10

4.1-11

4.1-13

rprojroot

1.3-2

1.2

1.3-1

1.3-2

1.2

Rsamtools

1.32.2

RSQLite

2.0

rstudioapi

0.7

0.9.0

0.7

R.utils

2.8.0

2.5.0

rvest

0.3.2

rzmq

0.9.3

S4Vectors

0.18.3

scales

0.5.0

1.0.0

0.5.0

selectr

0.3-1

0.4-1

0.3-1

sessioninfo

1.1.1

sfsmisc

1.1-1

shiny

1.3.0

1.0.5

snow

0.4-2

sourcetools

0.1.7

0.1.6

SparseM

1.77

spatial

7.3-11

splines

3.3.3

3.4.2

3.4.3

3.5.3

stats

3.3.3

3.4.2

3.4.3

3.5.3

stats4

3.3.3

3.4.2

3.4.3

3.5.3

stringi

1.1.6

1.1.5

1.1.6

1.4.3

1.1.5

stringr

1.2.0

1.4.0

1.2.0

survival

2.40-1

2.41-3

2.43-3

sys

3.1

tcltk

3.3.3

3.4.2

3.4.3

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

tidyr

0.7.2

0.8.0

0.7.2

0.8.3

0.7.2

tidyselect

0.2.3

0.2.5

0.2.3

tidyverse

1.2.1

timeDate

3042.101

tinytex

0.11

tools

3.3.3

3.4.2

3.4.3

3.5.3

TTR

0.23-2

usethis

1.4.0

utf8

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

uuid

0.1-2

viridisLite

0.2.0

0.3.0

0.2.0

whisker

0.3-2

withr

2.1.2

2.1.1

2.1.2

xfun

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

xtable

1.8-3

1.8-2

xts

0.11-2

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

Versions Compared

Old Version 25

New Version 26

Key

Which versions of R are available?

Usage

How to install R packages?

Installed Packages