R libraries

a4Base                                       Automated Affymetrix Array Analysis Base Package
a4Classif                                    Automated Affymetrix Array Analysis Classification Package
a4Core                                       Automated Affymetrix Array Analysis Core Package
a4Preproc                                    Automated Affymetrix Array Analysis Preprocessing Package
a4Reporting                                  Automated Affymetrix Array Analysis Reporting Package
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, plotsummary, plothulls, 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
aster                                        Aster Models
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
base64                                       Base 64 encoder/decoder
base64enc                                    Tools for base64 encoding
batchmeans                                   Consistent Batch Means Estimation of Monte Carlo Standard Errors
BayesLogit                                   Logistic Regression
baySeq                                       Empirical Bayesian analysis of patterns of differential expression in count data
bdsmatrix                                    Routines for Block Diagonal Symmetric matrices
beadarray                                    Quality assessment and low-level analysis for Illumina BeadArray data
BeadDataPackR                                Compression of Illumina BeadArray data
Benchmarking                                 Benchmark and frontier analysis using DEA and SFA
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
biom                                         An interface package (beta) for the BIOM file format.
biomaRt                                      Interface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase and Gramene)
biomod2                                      Ensemble platform for species distribution modeling
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.
CAMERA                                       Collection of annotation related methods for mass spectrometry data
car                                          Companion to Applied Regression
Category                                     Category Analysis
caTools                                      Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
cghFLasso                                    Detecting hot spot on CGH array data with fused lasso regression.
chron                                        Chronological objects which can handle dates and times
Ckmeans.1d.dp                                Optimal distance-based clustering for one-dimensional data
class                                        Functions for Classification
cluster                                      Cluster Analysis Extended Rousseeuw et al.
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
combinat                                     combinatorics utilities
compiler                                     The R Compiler Package
CompQuadForm                                 Distribution function of quadratic forms in normal variables
corpcor                                      Efficient Estimation of Covariance and (Partial) Correlation
coxme                                        Mixed Effects Cox Models.
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
deldir                                       Delaunay Triangulation and Dirichlet (Voronoi) Tessellation.
DESeq                                        Differential gene expression analysis based on the negative binomial distribution
DESeq2                                       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
dismo                                        Species distribution modeling
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
dynamicTreeCut                               Methods for detection of clusters in hierarchical clustering dendrograms.
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
expm                                         Matrix exponential
FactoMineR                                   Multivariate Exploratory Data Analysis and Data Mining with R
fastcluster                                  Fast hierarchical clustering routines for R and Python
fastmatch                                    Fast match() function
fda                                          Functional Data Analysis
fdrtool                                      Estimation of (Local) False Discovery Rates and Higher Criticism
ff                                           memory-efficient storage of large data on disk and fast access functions
ffbase                                       Basic statistical functions for package ff
flashClust                                   Implementation of optimal hierarchical clustering
foreach                                      Foreach looping construct for R
foreign                                      Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka, dBase, ...
Formula                                      Extended Model Formulas
gage                                         Generally Applicable Gene-set Enrichment for Pathway Analysis
gageData                                     Auxillary data for gage package
gam                                          Generalized Additive Models
gamm4                                        Generalized additive mixed models using mgcv and lme4
gbm                                          Generalized Boosted Regression Models
gcrma                                        Background Adjustment Using Sequence Information
gdata                                        Various R programming tools for data manipulation
gee                                          Generalized Estimation Equation solver
geiger                                       Analysis of evolutionary diversification
GeneCycle                                    Identification of Periodically Expressed Genes
genefilter                                   genefilter: methods for filtering genes from microarray experiments
GeneNet                                      Modeling and Inferring Gene Networks
geneplotter                                  Graphics related functions for Bioconductor
GenomicFeatures                              Tools for making and manipulating transcript centric annotations
GenomicRanges                                Representation and manipulation of genomic intervals
geoR                                         Analysis of geostatistical data
geoRglm                                      geoRglm - a package for generalised linear spatial models
getopt                                       C-like getopt behavior.
ggplot2                                      An implementation of the Grammar of Graphics
GLAD                                         Gain and Loss Analysis of DNA
glmmADMB                                     Generalized Linear Mixed Models using AD Model Builder
glmnet                                       Lasso and elastic-net regularized generalized linear models
gmm                                          Generalized Method of Moments and Generalized Empirical Likelihood
gmodels                                      Various R programming tools for model fitting
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
GPseq                                        gpseq: Using the generalized Poisson distribution to model sequence read counts from high
                                             throughput sequencing experiments
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
gregmisc                                     Greg's Miscellaneous Functions
grid                                         The Grid Graphics Package
gridExtra                                    functions in Grid graphics
grofit                                       The package was developed to fit fit many growth curves obtained under different
                                             conditions.
GSA                                          Gene set analysis
gsalib                                       Utility functions for GATK
GSEABase                                     Gene set enrichment data structures and methods
gsl                                          wrapper for the Gnu Scientific Library
gstat                                        spatial and spatio-temporal geostatistical modelling, prediction and simulation
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.
hexbin                                       Hexagonal Binning Routines
hglm                                         Hierarchical Generalized Linear Models
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)
hierNet                                      A Lasso for Hierarchical Interactions
HilbertVis                                   Hilbert curve visualization
Hmisc                                        Harrell Miscellaneous
HSAUR2                                       A Handbook of Statistical Analyses Using R (2nd Edition)
httr                                         Tools for working with URLs and HTTP
hwriter                                      HTML Writer - Outputs R objects in HTML format
igraph                                       Network analysis and visualization
illuminaio                                   Parsing Illumina microarray output files
impute                                       impute: Imputation for microarray data
INLA                                         Functions which allow to perform full Bayesian analysis of latent Gaussian models using
                                             Integrated Nested Laplace Approximaxion
inline                                       Inline C, C++, Fortran function calls from R
intervals                                    Tools for working with points and intervals
IRanges                                      Infrastructure for manipulating intervals on sequences
iterators                                    Iterator construct for R
itertools                                    Iterator Tools
jpeg                                         Read and write JPEG images
KEGG.db                                      A set of annotation maps for KEGG
KEGGgraph                                    KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KEGGREST                                     Client-side REST access to KEGG
KernSmooth                                   Functions for kernel smoothing for Wand & Jones (1995)
ks                                           Kernel smoothing
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
LearnBayes                                   Functions for Learning Bayesian Inference
limma                                        Linear Models for Microarray Data
lme4                                         Linear mixed-effects models using Eigen and S4
lmtest                                       Testing Linear Regression Models
locfit                                       Local Regression, Likelihood and Density Estimation.
longitudinal                                 Analysis of Multiple Time Course Data
LPCM                                         Local principal curve methods
lpridge                                      Local Polynomial (Ridge) Regression
lpSolveAPI                                   R Interface for lp_solve version 5.5.2.0
maanova                                      Tools for analyzing Micro Array experiments
magic                                        create and investigate magic squares
mapproj                                      Map Projections
maps                                         Draw Geographical Maps
maptools                                     Tools for reading and handling spatial objects
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
mboost                                       Model-Based Boosting
mclust                                       Normal Mixture Modeling for Model-Based Clustering, Classification, and Density
                                             Estimation
MCMCpack                                     Markov chain Monte Carlo (MCMC) Package
mda                                          Mixture and flexible discriminant analysis
memoise                                      Memoise functions
methods                                      Formal Methods and Classes
mgcv                                         Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation
minqa                                        Derivative-free optimization algorithms by quadratic approximation
misc3d                                       Miscellaneous 3D Plots
MLInterfaces                                 Uniform interfaces to R machine learning procedures for data in Bioconductor containers
mmap                                         Map Pages of Memory
mpm                                          Multivariate Projection Methods
msdata                                       Various Mass Spectrometry raw data example files
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
mzR                                          parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
ncbit                                        retrieve and build NBCI taxonomic data
ncdf                                         Interface to Unidata netCDF data files
ngspatial                                    Classes for Spatial Data
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
opm                                          Tools for analysing OmniLog(R) Phenotype Microarray data
org.Hs.eg.db                                 Genome wide annotation for Human
ouch                                         Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses
pamr                                         Pam: prediction analysis for microarrays
parallel                                     Support for Parallel computation in R
pathview                                     a tool set for pathway based data integration and visualization
permute                                      Functions for generating restricted permutations of data
pheatmap                                     Pretty Heatmaps
phyext                                       An extension of some of the classes in phylobase.  Tree objects now support subnodes on
                                             branches
phylobase                                    Base package for phylogenetic structures and comparative data
phyloseq                                     Handling and analysis of high-throughput microbiome census data.
picante                                      R tools for integrating phylogenies and ecology
pixmap                                       Bitmap Images (``Pixel Maps'')
pkgutils                                     pkgutils -- Utilities for creating R packages.
plier                                        Implements the Affymetrix PLIER algorithm
plotrix                                      Various plotting functions
pls                                          Partial Least Squares and Principal Component regression
plyr                                         Tools for splitting, applying and combining data
png                                          Read and write PNG images
polyclip                                     Polygon Clipping
pomp                                         Statistical inference for partially observed Markov processes
preprocessCore                               A collection of pre-processing functions
prettyR                                      Pretty descriptive stats.
pROC                                         display and analyze ROC curves
proftools                                    Profile Output Processing Tools for R
proj4                                        A simple interface to the PROJ.4 cartographic projections library
proto                                        Prototype object-based programming
PSCBS                                        Analysis of Parent-Specific DNA Copy Numbers
pscl                                         Political Science Computational Laboratory, Stanford University
ptw                                          Parametric Time Warping
quantreg                                     Quantile Regression
qvalue                                       Q-value estimation for false discovery rate control
R2admb                                       ADMB to R interface functions
R2jags                                       A Package for Running jags from R
R2WinBUGS                                    Running WinBUGS and OpenBUGS from R / S-PLUS
RandomFields                                 Simulation and Analysis of Random Fields
randomForest                                 Breiman and Cutler's random forests for classification and regression
RankProd                                     Rank Product method for identifying differentially expressed genes with application in
                                             meta-analysis
raster                                       raster: Geographic data analysis and modeling
rasterVis                                    Visualization methods for the raster package
RBGL                                         An interface to the BOOST graph library
R.cache                                      Fast and light-weight caching (memoization) of objects and results to speed up
                                             computations
Rcmdr                                        R Commander
RColorBrewer                                 ColorBrewer palettes
Rcpp                                         Seamless R and C++ Integration
RcppArmadillo                                Rcpp integration for Armadillo templated linear algebra library
RcppEigen                                    Rcpp integration for the Eigen templated linear algebra library.
RCurl                                        General network (HTTP/FTP/...) client interface for R
rda                                          Shrunken Centroids Regularized Discriminant Analysis
R.devices                                    Unified handling of graphics 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
rgdal                                        Bindings for the Geospatial Data Abstraction Library
rgeos                                        Interface to Geometry Engine - Open Source (GEOS)
rgl                                          3D visualization device system (OpenGL)
Rgraphviz                                    Provides plotting capabilities for R graph objects
R.huge                                       Methods for accessing huge amounts of data [DEPRECATED]
rjags                                        Bayesian graphical models using MCMC
rJava                                        Low-level R to Java interface
rjson                                        JSON for R
RJSONIO                                      Serialize R objects to JSON, JavaScript Object Notation
RMark                                        R Code for MARK Analysis
R.methodsS3                                  Utility function for defining S3 methods
RMySQL                                       R interface to the MySQL database
ROCR                                         Visualizing the performance of scoring classifiers.
R.oo                                         R object-oriented programming with or without references
rpart                                        Recursive Partitioning and Regression Trees
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: high-performance read alignment, quantification and mutation discovery
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
SemiPar                                      Semiparametic Regression
seqMeta                                      An R package for meta-analyzing region-based tests of rare DNA variants
setRNG                                       Set (Normal) Random Number Generator and Seed
sfsmisc                                      Utilities from Seminar fuer Statistik ETH Zurich
siggenes                                     Multiple testing using SAM and Efron's empirical Bayes approaches
simpleaffy                                   Very simple high level analysis of Affymetrix data
snow                                         Simple Network of Workstations
snowfall                                     Easier cluster computing (based on snow).
SNPchip                                      Visualizations for copy number alterations
sp                                           classes and methods for spatial data
spacetime                                    classes and methods for spatio-temporal data
spam                                         SPArse Matrix
SparseM                                      Sparse Linear Algebra
spatial                                      Functions for Kriging and Point Pattern Analysis
spatial.tools                                R functions for working with spatial data.
spatstat                                     Spatial Point Pattern analysis, model-fitting, simulation, tests
spBayes                                      Univariate and Multivariate Spatial-temporal Modeling
spdep                                        Spatial dependence: weighting schemes, statistics and models
splancs                                      Spatial and Space-Time Point Pattern Analysis
splines                                      Regression Spline Functions and Classes
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
SVGAnnotation                                Tools for post-processing SVG plots created in R
tcltk                                        Tcl/Tk Interface
tcltk2                                       Tcl/Tk Additions
tensor                                       Tensor product of arrays
TH.data                                      TH's Data Archive
tilingArray                                  Transcript mapping with high-density oligonucleotide tiling arrays
tmvtnorm                                     Truncated Multivariate Normal and Student t Distribution
tools                                        Tools for Package Development
truncnorm                                    Truncated normal distribution
trust                                        Trust Region Optimization
ucminf                                       General-purpose unconstrained non-linear optimization
unmarked                                     Models for Data from Unmarked Animals
utils                                        The R Utils Package
varSelRF                                     Variable selection using random forests
vcd                                          Visualizing Categorical Data
vegan                                        Community Ecology Package
VGAM                                         Vector Generalized Linear and Additive Models
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.
WGCNA                                        Weighted Correlation Network Analysis
xcms                                         LC/MS and GC/MS Data Analysis
XML                                          Tools for parsing and generating XML within R and S-Plus.
xtable                                       Export tables to LaTeX or HTML
xts                                          eXtensible Time Series
XVector                                      Representation and manpulation of external sequences
yaml                                         Methods to convert R data to YAML and back
zlibbioc                                     An R packaged zlib-1.2.5
zoo                                          S3 Infrastructure for Regular and Irregular Time Series (Z's ordered observations)