Difference between revisions of "R"

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Line 88: Line 88:
ggplot2                An implementation of the Grammar of Graphics
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
GO.db                  A set of annotation maps describing the entire
                         Gene Ontology
                         Gene Ontology

Revision as of 17:28, 16 January 2012


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

Available versions

  • 2.13.1

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

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
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
genefilter              genefilter: methods for filtering genes from
                        microarray experiments
geneplotter             Graphics related functions for Bioconductor
GenomicRanges           Representation and manipulation of genomic
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
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
lattice                 Lattice Graphics
leaps                   regression subset selection
limma                   Linear Models for Microarray Data
locfit                  Local Regression, Likelihood and Density
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
preprocessCore          A collection of pre-processing functions
prettyR                 Pretty descriptive stats.
proto                   Prototype object-based programming
qvalue                  Q-value estimation for false discovery rate
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
spatial                 Functions for Kriging and Point Pattern
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
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