R libraries

abind                   Combine multi-dimensional arrays
aCGH                    Classes and functions for Array Comparative
                        Genomic Hybridization data.
ade4                    Analysis of Ecological Data : Exploratory and
                        Euclidean methods in Environmental sciences
affxparser              Affymetrix File Parsing SDK
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
Agi4x44PreProcess       PreProcessing of Agilent 4x44 array data
agricolae               Statistical Procedures for Agricultural
                        Research
akima                   Interpolation of irregularly spaced data
annaffy                 Annotation tools for Affymetrix biological
                        metadata
annotate                Annotation for microarrays
AnnotationDbi           Annotation Database Interface
AnnotationForge         Code for Building Annotation Database Packages
ape                     Analyses of Phylogenetics and Evolution
aplpack                 Another Plot PACKage: stem.leaf, bagplot,
                        faces, spin3R, and some slider functions
aroma.affymetrix        Analysis of large Affymetrix microarray data
                        sets
aroma.apd               A probe-level data file format used by
                        aroma.affymetrix [DEPRECATED]
aroma.core              Core methods and classes used by aroma.*
                        packages part of The Aroma Framework
aroma.light             Light-weight methods for normalization and
                        visualization of microarray data using only
                        basic R data types
arrayQualityMetrics     Quality metrics on microarray data sets
auteur                  Bayesian sampler of the trait-evolutionary
                        process
aws                     Adaptive Weights Smoothing
awsMethods              Class and Methods definitions for packages aws,
                        adimpro, fmri, dwi
BAMD                    Bayesian Association Model for Genomic Data
                        with Missing Covariates
base                    The R Base Package
baySeq                  Empirical Bayesian analysis of patterns of
                        differential expression in count data
beadarray               Quality assessment and low-level analysis for
                        Illumina BeadArray data
BeadDataPackR           Compression of Illumina BeadArray data
binom                   Binomial Confidence Intervals For Several
                        Parameterizations
Biobase                 Biobase: Base functions for Bioconductor
BiocGenerics            Generic functions for Bioconductor
BiocInstaller           Install/Update Bioconductor and CRAN Packages
biomaRt                 Interface to BioMart databases (e.g. Ensembl,
                        COSMIC ,Wormbase and Gramene)
Biostrings              String objects representing biological
                        sequences, and matching algorithms
abind                   Combine multi-dimensional arrays
aCGH                    Classes and functions for Array Comparative
                        Genomic Hybridization data.
ade4                    Analysis of Ecological Data : Exploratory and
                        Euclidean methods in Environmental sciences
affxparser              Affymetrix File Parsing SDK
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
Agi4x44PreProcess       PreProcessing of Agilent 4x44 array data
agricolae               Statistical Procedures for Agricultural
                        Research
akima                   Interpolation of irregularly spaced data
annaffy                 Annotation tools for Affymetrix biological
                        metadata
annotate                Annotation for microarrays
AnnotationDbi           Annotation Database Interface
AnnotationForge         Code for Building Annotation Database Packages
ape                     Analyses of Phylogenetics and Evolution
aplpack                 Another Plot PACKage: stem.leaf, bagplot,
                        faces, spin3R, and some slider functions
aroma.affymetrix        Analysis of large Affymetrix microarray data
                        sets
aroma.apd               A probe-level data file format used by
                        aroma.affymetrix [DEPRECATED]
aroma.core              Core methods and classes used by aroma.*
                        packages part of The Aroma Framework
aroma.light             Light-weight methods for normalization and
                        visualization of microarray data using only
                        basic R data types
arrayQualityMetrics     Quality metrics on microarray data sets
auteur                  Bayesian sampler of the trait-evolutionary
                        process
aws                     Adaptive Weights Smoothing
awsMethods              Class and Methods definitions for packages aws,
                        adimpro, fmri, dwi
BAMD                    Bayesian Association Model for Genomic Data
                        with Missing Covariates
base                    The R Base Package
baySeq                  Empirical Bayesian analysis of patterns of
                        differential expression in count data
beadarray               Quality assessment and low-level analysis for
                        Illumina BeadArray data
BeadDataPackR           Compression of Illumina BeadArray data
binom                   Binomial Confidence Intervals For Several
                        Parameterizations
Biobase                 Biobase: Base functions for Bioconductor
BiocGenerics            Generic functions for Bioconductor
BiocInstaller           Install/Update Bioconductor and CRAN Packages
biomaRt                 Interface to BioMart databases (e.g. Ensembl,
                        COSMIC ,Wormbase and Gramene)
Biostrings              String objects representing biological
                        sequences, and matching algorithms
biovizBase              Basic graphic utilities for visualization of
                        genomic data.
bit                     A class for vectors of 1-bit booleans
bitops                  Bitwise Operations
boot                    Bootstrap Functions (originally by Angelo Canty
                        for S)
BSgenome                Infrastructure for Biostrings-based genome data
                        packages
Cairo                   R graphics device using cairo graphics library
                        for creating high-quality bitmap (PNG, JPEG,
                        TIFF), vector (PDF, SVG, PostScript) and
                        display (X11 and Win32) output.
car                     Companion to Applied Regression
Category                Category Analysis
caTools                 Tools: moving window statistics, GIF, Base64,
                        ROC AUC, etc.
ce25bmrv02cdf           ce25bmrv02cdf
cghFLasso               Detecting hot spot on CGH array data with fused
                        lasso regression.
CGHweb                  analyzing array_CGH data with multiple
                        algorithms
chron                   Chronological objects which can handle dates
                        and times
class                   Functions for Classification
cluster                 Cluster Analysis Extended Rousseeuw et al.
cnv                     Detection of Copy Number Variation by
                        Sequencing
CNVtools                A package to test genetic association with CNV
                        data
coda                    Output analysis and diagnostics for MCMC
codetools               Code Analysis Tools for R
colorspace              Color Space Manipulation
compiler                The R Compiler Package
crlmm                   Genotype Calling (CRLMM) and Copy Number
                        Analysis tool for Affymetrix SNP 5.0 and 6.0
                        and Illumina arrays.
cummeRbund              Analysis, exploration, manipulation, and
                        visualization of Cufflinks high-throughput
                        sequencing data.
datasets                The R Datasets Package
DBI                     R Database Interface
DESeq                   Differential gene expression analysis based on
                        the negative binomial distribution
deSolve                 General solvers for initial value problems of
                        ordinary differential equations (ODE), partial
                        differential equations (PDE), differential
                        algebraic equations (DAE), and delay
                        differential equations (DDE).
DEXSeq                  Inference of differential exon usage in RNA-Seq
dichromat               Color schemes for dichromats
digest                  Create cryptographic hash digests of R objects
diversitree             diversitree: comparative phylogenetic analyses
                        of diversification
DNAcopy                 DNA copy number data analysis
doMC                    Foreach parallel adaptor for the multicore
                        package
doParallel              Foreach parallel adaptor for the parallel
                        package
doSNOW                  Foreach parallel adaptor for the snow package
DynDoc                  Dynamic document tools
e1071                   Misc Functions of the Department of Statistics
                        (e1071), TU Wien
edgeR                   Empirical analysis of digital gene expression
                        data in R
effects                 Effect Displays for Linear, Generalized Linear,
                        Multinomial-Logit, Proportional-Odds Logit
                        Models and Mixed-Effects Models
ellipse                 Functions for drawing ellipses and ellipse-like
                        confidence regions
EMA                     Easy Microarray data Analysis
exonmap                 High level analysis of Affymetrix exon array
                        data
exon.pmcdf              exon.pmcdf
FactoMineR              Multivariate Exploratory Data Analysis and Data
                        Mining with R
FASeg                   Forward-backward fragment assembling method for
                        the segmentation of array-based copy number
                        data
fastcluster             Fast hierarchical clustering routines for R and
                        Python
fda                     Functional Data Analysis
ff                      memory-efficient storage of large data on disk
                        and fast access functions
foreach                 Foreach looping construct for R
foreign                 Read Data Stored by Minitab, S, SAS, SPSS,
                        Stata, Systat, dBase, ...
gcrma                   Background Adjustment Using Sequence
                        Information
gdata                   Various R programming tools for data
                        manipulation
GDD                     GD device for creating bitmap graphics as jpeg,
                        png or gif files using gd library
gee                     Generalized Estimation Equation solver
geiger                  Analysis of evolutionary diversification
genefilter              genefilter: methods for filtering genes from
                        microarray experiments
geneplotter             Graphics related functions for Bioconductor
GenomicFeatures         Tools for making and manipulating transcript
                        centric annotations
GenomicRanges           Representation and manipulation of genomic
                        intervals
ggplot2                 An implementation of the Grammar of Graphics
GLAD                    Gain and Loss Analysis of DNA
glmmADMB                Generalized Linear Mixed Models using AD Model
                        Builder
GO.db                   A set of annotation maps describing the entire
                        Gene Ontology
GOstats                 Tools for manipulating GO and microarrays.
gplots                  Various R programming tools for plotting data
graph                   graph: A package to handle graph data
                        structures
graphics                The R Graphics Package
grDevices               The R Graphics Devices and Support for Colours
                        and Fonts
grid                    The Grid Graphics Package
GSA                     Gene set analysis
GSEABase                Gene set enrichment data structures and methods
gsubfn                  Utilities for strings and function arguments.
gtable                  Arrange grobs in tables.
gtools                  Various R programming tools
Gviz                    Plotting data and annotation information along
                        genomic coordinates
heatmap.plus            Heatmap with more sensible behavior.
hgu133plus2.db          Affymetrix Human Genome U133 Plus 2.0 Array
                        annotation data (chip hgu133plus2)
hgu95av2.db             Affymetrix Human Genome U95 Set annotation data
                        (chip hgu95av2)
HilbertVis              Hilbert curve visualization
Hmisc                   Harrell Miscellaneous
HSAUR2                  A Handbook of Statistical Analyses Using R (2nd
                        Edition)
hwriter                 HTML Writer - Outputs R objects in HTML format
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)
labeling                Axis Labeling
lars                    Least Angle Regression, Lasso and Forward
                        Stagewise
laser                   Likelihood Analysis of Speciation/Extinction
                        Rates from Phylogenies
lattice                 Lattice Graphics
latticeExtra            Extra Graphical Utilities Based on Lattice
leaps                   regression subset selection
limma                   Linear Models for Microarray Data
lme4                    Linear mixed-effects models using S4 classes
lmtest                  Testing Linear Regression Models
locfit                  Local Regression, Likelihood and Density
                        Estimation.
lpridge                 Local Polynomial (Ridge) Regression
maanova                 Tools for analyzing Micro Array experiments
maDB                    Microarray database and utility functions for
                        microarray data analysis.
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
matrixcalc              Collection of functions for matrix calculations
matrixStats             Methods that apply to rows and columns of a
                        matrix
mclust                  Normal Mixture Modeling for Model-Based
                        Clustering, Classification, and Density
                        Estimation
MCMCpack                Markov chain Monte Carlo (MCMC) Package
memoise                 Memoise functions
methods                 Formal Methods and Classes
mgcv                    Mixed GAM Computation Vehicle with GCV/AIC/REML
                        smoothness estimation
msm                     Multi-state Markov and hidden Markov models in
                        continuous time
multcomp                Simultaneous Inference in General Parametric
                        Models
multicore               Parallel processing of R code on machines with
                        multiple cores or CPUs
multtest                Resampling-based multiple hypothesis testing
munsell                 Munsell colour system
MVA                     An Introduction to Applied Multivariate
                        Analysis with R
mvtnorm                 Multivariate Normal and t Distributions
nlme                    Linear and Nonlinear Mixed Effects Models
nnet                    Feed-forward Neural Networks and Multinomial
                        Log-Linear Models
oligoClasses            Classes for high-throughput arrays supported by
                        oligo and crlmm
org.Hs.eg.db            Genome wide annotation for Human
ouch                    Ornstein-Uhlenbeck models for phylogenetic
                        comparative hypotheses
parallel                Support for Parallel computation in R
permute                 Functions for generating restricted
                        permutations of data
pgUtils                 Utility functions for PostgreSQL databases
pheatmap                Pretty Heatmaps
phylobase               Base package for phylogenetic structures and
                        comparative data
picante                 R tools for integrating phylogenies and ecology
pixmap                  Bitmap Images (``Pixel Maps'')
plier                   Implements the Affymetrix PLIER algorithm
plotrix                 Various plotting functions
plyr                    Tools for splitting, applying and combining
                        data
preprocessCore          A collection of pre-processing functions
prettyR                 Pretty descriptive stats.
proto                   Prototype object-based programming
PSCBS                   Analysis of Parent-Specific DNA Copy Numbers
quantreg                Quantile Regression
qvalue                  Q-value estimation for false discovery rate
                        control
R2admb                  ADMB to R interface functions
RankProd                Rank Product method for identifying
                        differentially expressed genes with application
                        in meta-analysis
RBGL                    An interface to the BOOST graph library
R.cache                 Fast and light-weight caching (memoization) of
                        objects
Rcmdr                   R Commander
RColorBrewer            ColorBrewer palettes
Rcpp                    Seamless R and C++ Integration
RcppEigen               Rcpp integration for the Eigen templated linear
                        algebra library.
RCurl                   General network (HTTP/FTP/...) client interface
                        for R
R.devices               Enhanced methods for handling graphical devices
relimp                  Relative Contribution of Effects in a
                        Regression Model
reshape                 Flexibly reshape data.
reshape2                Flexibly reshape data: a reboot of the reshape
                        package.
R.filesets              Easy handling of and access to files organized
                        in structured directories
rgl                     3D visualization device system (OpenGL)
R.huge                  Methods for accessing huge amounts of data
                        [DEPRECATED]
RMark                   R Code for MARK Analysis
R.methodsS3             Utility function for defining S3 methods
RMySQL                  R interface to the MySQL database
R.oo                    R object-oriented programming with or without
                        references
rpart                   Recursive Partitioning
RPostgreSQL             R interface to the PostgreSQL database system
R.rsp                   Dynamic generation of scientific reports
Rsamtools               Binary alignment (BAM), variant call (BCF), or
                        tabix file import
RSQLite                 SQLite interface for R
RSQLite.extfuns         Math and String Extension Functions for RSQLite
Rsubread                Rsubread: a super fast, sensitive and accurate
                        read aligner for mapping next-generation
                        sequencing reads
rtracklayer             R interface to genome browsers and their
                        annotation tracks
R.utils                 Various programming utilities
Rwave                   Time-Frequency analysis of 1-D signals
sandwich                Robust Covariance Matrix Estimators
scales                  Scale functions for graphics.
scatterplot3d           3D Scatter Plot
sem                     Structural Equation Models
setRNG                  Set (Normal) Random Number Generator and Seed
siggenes                Multiple testing using SAM and Efron's
                        empirical Bayes approaches
simpleaffy              Very simple high level analysis of Affymetrix
                        data
smida                   Statistics for Microarrays: Inference, Design
                        and Analysis
snapCGH                 Segmentation, normalisation and processing of
                        aCGH data.
snow                    Simple Network of Workstations
snowfall                Easier cluster computing (based on snow).
SNPchip                 Visualizations for copy number alterations
SparseM                 Sparse Linear Algebra
spatial                 Functions for Kriging and Point Pattern
                        Analysis
splines                 Regression Spline Functions and Classes
spp                     some description
sqldf                   Perform SQL Selects on R Data Frames
statmod                 Statistical Modeling
stats                   The R Stats Package
stats4                  Statistical Functions using S4 Classes
stringr                 Make it easier to work with strings.
strucchange             Testing, Monitoring, and Dating Structural
                        Changes
subplex                 Subplex optimization algorithm
survival                Survival analysis, including penalised
                        sequencing reads
rtracklayer             R interface to genome browsers and their
                        annotation tracks
R.utils                 Various programming utilities
Rwave                   Time-Frequency analysis of 1-D signals
sandwich                Robust Covariance Matrix Estimators
scales                  Scale functions for graphics.
scatterplot3d           3D Scatter Plot
sem                     Structural Equation Models
setRNG                  Set (Normal) Random Number Generator and Seed
siggenes                Multiple testing using SAM and Efron's
                        empirical Bayes approaches
simpleaffy              Very simple high level analysis of Affymetrix
                        data
smida                   Statistics for Microarrays: Inference, Design
                        and Analysis
snapCGH                 Segmentation, normalisation and processing of
                        aCGH data.
snow                    Simple Network of Workstations
snowfall                Easier cluster computing (based on snow).
SNPchip                 Visualizations for copy number alterations
SparseM                 Sparse Linear Algebra
spatial                 Functions for Kriging and Point Pattern
                        Analysis
splines                 Regression Spline Functions and Classes
spp                     some description
sqldf                   Perform SQL Selects on R Data Frames
statmod                 Statistical Modeling
stats                   The R Stats Package
stats4                  Statistical Functions using S4 Classes
stringr                 Make it easier to work with strings.
strucchange             Testing, Monitoring, and Dating Structural
                        Changes
subplex                 Subplex optimization algorithm
survival                Survival analysis, including penalised
                        likelihood.
SVGAnnotation           Tools for post-processing SVG plots created in
                        R
tcltk                   Tcl/Tk Interface
tilingArray             Transcript mapping with high-density
                        oligonucleotide tiling arrays
tools                   Tools for Package Development
truncnorm               Truncated normal distribution
utils                   The R Utils Package
vegan                   Community Ecology 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
zlibbioc                An R packaged zlib-1.2.5
zoo                     S3 Infrastructure for Regular and Irregular
                        Time Series (Z's ordered observations)