R (statistical computing)

A popular, full featured, statistical computing package

Introduction

The "R" Tool is an open-source, popular, and fully-featured statistical application and programming platform. We have multiple R versions installed on HPC.

Running R on RCC Systems

To enter an interactive R session on HPC or Spear, simply "R" command.  The default version that loads is Version 3.4.0.  If you wish to run an older version, you must load the appropriate module before running "R"; e.g.:

# loads version 3.2.5
module load R/3.2.5

# loads version 3.2.0
module load R/3.2.0

Type 'q()' to quit R.

To submit R jobs to SLURM, refer to the following example submission script:

#!/bin/bash

#SBATCH -n 1
#SBATCH -J "MyRJob"
#SBATCH -p backfill
#SBATCH -t 1:00:00
#SBATCH --mail-type=ALL

module load R/3.2.5

R CMD BATCH yourRscript

The yourRscript is a text file where you have saved R commands to run.

For more information about R, refer to the online documentation

Available Packages

RCC has an extensive list of packages for R available.

List of Available R Packages

  • Akima
  • acepack
  • ade4
  • ald
  • assertthat
  • backports
  • base
  • base64enc
  • BH
  • bitops
  • boot
  • Brew
  • caTools
  • checkmate
  • chron
  • class
  • cluster
  • coda
  • codetools
  • colorspace
  • compiler
  • crayon
  • curl
  • datasets
  • data.table
  • DBI
  • dichromat
  • digest
  • doParallel
  • doSNOW
  • evaluate
  • fdasrvf
  • fields
  • foreach
  • foreign
  • Formula
  • futile.logger
  • futile.options
  • gdata
  • grDevices
  • graphics
  • grid
  • ggplot2
  • ghyp
  • gplots
  • graph
  • gridExtra
  • gtable
  • gtools
  • hexbin
  • highr
  • Hmisc
  • htmlTable
  • htmltools
  • htmlwidgets
  • httr
  • hwriter
  • iterators
  • jsonlite
  • KernSmooth
  • knitr
  • labeling
  • lambda.r
  • Lattice
  • latticeExtra
  • lava
  • lazyeval
  • locfit
  • MADAM
  • magrittr
  • manipulate
  • maps
  • markdown
  • MASS
  • matrix
  • matrixcalc
  • MatrixModels
  • matrixStats
  • memoise
  • methods
  • mgcv
  • mime
  • mnormt
  • munsell
  • mvtnorm
  • numDeriv
  • nnet
  • openintro
  • openssl
  • parellel
  • plogr
  • plyr
  • praise
  • psych
  • qrLMM
  • quantreg
  • R6
  • RColorBrewer
  • RcppArmadillo
  • Rcpp
  • RCurl
  • reshape2
  • rjags
  • rlang
  • rpart
  • RSQLite
  • scales
  • scatterplot3d
  • sendmailR
  • snow
  • spam
  • SparseM
  • spatial
  • splines
  • statmod
  • stats
  • stats4
  • stringi
  • stringr
  • survival
  • swirl
  • testthat
  • tibble
  • timereg
  • tools
  • utils
  • viridisLite
  • viridis
  • XML
  • xtable
  • yaml

Bioconductor on RCC Systems

Bioconductor is a very extensive set of libraries and tools written in R for use in R programs which are designed to perform a myriad of different tasks common to bioinformatics data analysis. RCC has an extensive list of Bioconductor packages installed for use on RCC Systems. A complete list of these follows in the section below.

List of Available Bioconductor Packages

  • affiyo
  • affy
  • annaffy
  • annotate
  • annotationDbi
  • Biobase
  • BiocInstaller
  • BiocGenerics
  • BiocParallel
  • biomaRt
  • Biostrings
  • DelayedArray
  • DESeq
  • DESeq2
  • DEXSeq
  • gcrma
  • genefilter
  • geneplotter
  • GenomeInfoDbData
  • GenomeInfoDb
  • GenomicAlignments
  • GenomicFeatures
  • GenomicRanges
  • GO.db
  • iRanges
  • KEGG.db
  • KEGGgraph
  • limma
  • made4
  • multtest
  • preprocessCore
  • qvalue
  • Rgraphviz
  • Rsamtools
  • rtracklayer
  • S4Vectors
  • SPIA
  • SummarizedExperiment
  • vsn
  • webbioc
  • XVector
  • zlibbioc