# R

Revision as of 18:11, 27 February 2012 by Moskalenko (talk | contribs)

## Description

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R is a free software environment for statistical computing and graphics.
Template:App Location

## Available versions

**Note: File a support ticket to request installation of additional libraries.**

- 2.13.1
- 2.14.1 (default)
- 2.14.1 - R base package MPI-enabled via the Rmpi library.

## Running the application using modules

To use R with the environment modules system at HPC the following commands are available:

Get module information for r:

$module spider R

Load the default application module:

$module load R

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

- HPC_R_DIR - directory where R is located.
- HPC_R_BIN - executable directory
- HPC_R_LIB - library directory
- HPC_R_INCLUDE - includes directory

To use the version of R built for parallel execution with MPI via the Rmpi library load the following modules:

module load intel/11.1 openmpi/1.4.3 R

## Installed Packages

**Note: ** Many of the packages in the R library shown below are installed as a part of Bioconductor meta-library.

affy Methods for Affymetrix Oligonucleotide Arrays affydata Affymetrix Data for Demonstration Purpose affyio Tools for parsing Affymetrix data files affyPLM Methods for fitting probe-level models affyQCReport QC Report Generation for affyBatch objects akima Interpolation of irregularly spaced data annaffy Annotation tools for Affymetrix biological metadata annotate Annotation for microarrays AnnotationDbi Annotation Database Interface base The R Base Package baySeq Empirical Bayesian analysis of patterns of differential expression in count data Biobase Biobase: Base functions for Bioconductor Biostrings String objects representing biological sequences, and matching algorithms bitops Functions for Bitwise operations boot Bootstrap Functions (originally by Angelo Canty for S) class Functions for Classification cluster Cluster Analysis Extended Rousseeuw et al. codetools Code Analysis Tools for R colorspace Color Space Manipulation compiler The R Compiler Package datasets The R Datasets Package DBI R Database Interface DESeq Digital gene expresion analysis based on the negative binomial distribution digest Create cryptographic hash digests of R objects DynDoc Dynamic document tools edgeR Empirical analysis of digital gene expression data in R foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ... gcrma Background Adjustment Using Sequence Information genefilter genefilter: methods for filtering genes from microarray experiments geneplotter Graphics related functions for Bioconductor GenomicRanges Representation and manipulation of genomic intervals ggplot2 An implementation of the Grammar of Graphics glmmADMB Fitting generalized linear mixed models (GLMMs) GO.db A set of annotation maps describing the entire Gene Ontology graphics The R Graphics Package grDevices The R Graphics Devices and Support for Colours and Fonts grid The Grid Graphics Package hgu95av2.db Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) HilbertVis Hilbert curve visualization Hmisc Harrell Miscellaneous IRanges Infrastructure for manipulating intervals on sequences iterators Iterator construct for R itertools Iterator Tools KEGG.db A set of annotation maps for KEGG KernSmooth Functions for kernel smoothing for Wand & Jones (1995) lattice Lattice Graphics leaps regression subset selection limma Linear Models for Microarray Data locfit Local Regression, Likelihood and Density Estimation. marray Exploratory analysis for two-color spotted microarray data MASS Support Functions and Datasets for Venables and Ripley's MASS Matrix Sparse and Dense Matrix Classes and Methods methods Formal Methods and Classes mgcv GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL multtest Resampling-based multiple hypothesis testing nlme Linear and Nonlinear Mixed Effects Models nnet Feed-forward Neural Networks and Multinomial Log-Linear Models org.Hs.eg.db Genome wide annotation for Human plyr Tools for splitting, applying and combining data preprocessCore A collection of pre-processing functions prettyR Pretty descriptive stats. proto Prototype object-based programming qvalue Q-value estimation for false discovery rate control RColorBrewer ColorBrewer palettes reshape Flexibly reshape data. rpart Recursive Partitioning RSQLite SQLite interface for R Rtwalk Sampling from many objective functions Rwave Time-Frequency analysis of 1-D signals simpleaffy Very simple high level analysis of Affymetrix data spatial Functions for Kriging and Point Pattern Analysis splines Regression Spline Functions and Classes statmod Statistical Modeling stats The R Stats Package stats4 Statistical Functions using S4 Classes survival Survival analysis, including penalised likelihood. tcltk Tcl/Tk Interface tools Tools for Package Development utils The R Utils Package vsn Variance stabilization and calibration for microarray data waveslim Basic wavelet routines for one-, two- and three-dimensional signal processing wavethresh Wavelets statistics and transforms. XML Tools for parsing and generating XML within R and S-Plus. xtable Export tables to LaTeX or HTML