Package Index

Packages in the standard library

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

adSplit Annotation-Driven Clustering

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

amap Another Multidimensional Analysis Package

annaffy Annotation tools for Affymetrix biological metadata

annotate Annotation for microarrays

AnnotationDbi Annotation Database Interface

ape Analyses of Phylogenetics and Evolution

aws Adaptive Weights Smoothing

base The R Base Package

bayesmix Bayesian Mixture Models with JAGS

beadarraySNP Normalization and reporting of Illumina SNP bead arrays

BeadExplorer QC, normalisation, annotation and exploration of Illumina BeadChip data

Biobase Biobase: Base functions for Bioconductor

bioDist Different distance measures

biomaRt Interface to BioMart databases (e.g. Ensembl, Wormbase and Gramene)

Biostrings String objects representing biological sequences, and matching algorithms

bitops Functions for Bitwise operations

boot Bootstrap R (S-Plus) Functions (Canty)

BSgenome Infrastructure for Biostrings-based genome data packages

car Companion to Applied Regression

Category Category Analysis

caTools Tools: moving window statistics, GIF, Base64, ROC AUC, etc.

celsius Retrieve Affymetrix microarray measurements and metadata from Celsius

ChromoViz Multimodal visualization of gene expression data

class Functions for Classification

cluster Cluster Analysis Extended Rousseeuw et al.

coda Output analysis and diagnostics for MCMC

codetools Code Analysis Tools for R

combinat combinatorics utilities

corpcor Efficient Estimation of Covariance and (Partial) Correlation

cosmo Supervised detection of conserved motifs in DNA sequences

ctc Cluster and Tree Conversion.

datasets The R Datasets Package

DBI R Database Interface

degreenet Models for Skewed Count Distributions Relevant to Networks

Design Design Package

DynDoc Dynamic document tools

ergm Fit, Simulate and Diagnose Exponential-Family Models for Networks

exonmap High level analysis of Affymetrix exon array data

fastICA FastICA Algorithms to perform ICA and Projection Pursuit

fdrtool Estimation and Control of (Local) False Discovery Rates

fields Tools for spatial data

flexclust Flexible Cluster Algorithms

flexmix Flexible Mixture Modeling

foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ...

fork R functions for handling multiple processes.

gaschYHS ExpressionSet for response of yeast to heat shock and other environmental stresses

gcrma Background Adjustment Using Sequence Information

gdata Various R programming tools for data manipulation

gee Generalized Estimation Equation solver

GenABEL genome-wide SNP association analysis

GeneCycle Identification of Periodically Expressed Genes

genefilter genefilter: methods for filtering genes from microarray experiments

GeneNet Modeling and Inferring Gene Networks

geneplotter Grapics related functions for Bioconductor

genetics Population Genetics

GeneTS Microarray Time Series and Network Analysis

GEOquery Get data from NCBI Gene Expression Omnibus (GEO)

GGBase infrastructure for genetics of gene expression (c) 2008 VJ Carey

ggplot An implementation of the Grammar of Graphics in R

ggplot2 An implementation of the Grammar of Graphics

GGtools software and data for genetical genomics (c) 2006 VJ Carey

GLAD Gain and Loss Analysis of DNA

GO A data package containing annotation data for GO

GO.db A set of annotation maps describing the entire Gene Ontology

goTools Functions for Gene Ontology database

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

GSEABase Gene set enrichment data structures and methods

gtools Various R programming tools

hapassoc Inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm

haplo.stats Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

HardyWeinberg Graphical tests for Hardy-Weinberg equilibrium

hgfocus Affymetrix Human Genome Focus Array Annotation Data (hgfocus)

hgu95av2 Affymetrix Human Genome U95 Set Annotation Data (hgu95av2)

Hmisc Harrell Miscellaneous

hopach Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

hwde Models and tests for departure from Hardy-Weinberg equilibrium and independence between loci.

ibdreg Regression Methods for IBD Linkage With Covariates

Icens NPMLE for Censored and Truncated Data

impute impute: Imputation for microarray data

IRanges Low-level containers for storing sets of integer ranges

KEGG A data package containing annotation data for KEGG

KEGG.db A set of annotation maps for KEGG

KEGGSOAP Client-side SOAP access KEGG

KernSmooth Functions for kernel smoothing for Wand & Jones (1995)

latentnet Latent position and cluster models for statistical networks

lattice Lattice Graphics

limma Linear Models for Microarray Data

lodplot Plot a genome scan

logicFS Identification of SNP Interactions

LogicReg Logic Regression

longitudinal Analysis of Multiple Time Course Data

lumi BeadArray Specific Methods for Illumina Microarrays

made4 Multivariate analysis of microarray data using ADE4

mapLD Linkage Disequilibrium Mapping

maps Draw Geographical Maps

marray Exploratory analysis for two-color spotted microarray data

MASS Main Package of Venables and Ripley's MASS

matchprobes Basic infrastructure for using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment

Matrix Sparse and Dense Matrix Classes and Methods

mclust Model-Based Clustering / Normal Mixture Modeling

methods Formal Methods and Classes

mgcv GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL

mgu74av2 Affymetrix Murine Genome U74v2 Annotation Data (mgu74av2)

modeltools Tools and Classes for Statistical Models

msm Multi-state Markov and hidden Markov models in continuous time

multcomp Simultaneous Inference in General Parametric Models

multtest Resampling-based multiple hypothesis testing

mvtnorm Multivariate Normal and t Distributions

network Classes for Relational Data

networksis Simulate bipartite graphs with fixed marginals through sequential importance sampling

nlme Linear and Nonlinear Mixed Effects Models

nnet Feed-forward Neural Networks and Multinomial Log-Linear Models

odesolve Solvers for Ordinary Differential Equations

oligoClasses Classes for high-throughput SNP arrays

pcaPP Robust PCA by Projection Pursuit

pixmap Bitmap Images (``Pixel Maps'')

plier Implements the Affymetrix PLIER algorithm

plotrix Various plotting functions

plyr Tools for splitting, applying and combining data

prada Data analysis for cell-based functional assays

preprocessCore A collection of pre-processing functions

proftools Profile Output Processing Tools for R

proto Prototype object-based programming

pvclust Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling

quadprog Functions to solve Quadratic Programming Problems.

quantreg Quantile Regression

quantsmooth Quantile smoothing and genomic visualization of array data

qvalue Q-value estimation for false discovery rate control

R2HTML HTML exportation for R objects

RankProd Rank Product method for identifying differentially expressed genes with application in meta-analysis

RBGL An interface to the BOOST graph library

RColorBrewer ColorBrewer palettes

RCurl HTTP request interface

Rdonlp2 an R extension library to use Peter Spelluci's DONLP2 from R.

reshape Flexibly reshape data.

rgl 3D visualization device system (OpenGL)

Rgraphviz Provides plotting capabilities for R graph objects

Ringo R Investigation of ChIP-chip Oligoarrays

rJava Low-level R to Java interface

RMesquite Wrapper for Mesquite methods in R

RMySQL R interface to the MySQL database

robustbase Basic Robust Statistics

ROC utilities for ROC, with uarray focus

Rolexa Statistical analysis of Solexa sequencing data

Rolexa.demo Demo data for the Rolexa package

rpart Recursive Partitioning

rrcov Scalable Robust Estimators with High Breakdown Point

RSPerl The Omegahat interface for R and Perl.

RSQLite SQLite interface for R

RSvgDevice An R SVG graphics device.

rtracklayer R interface to genome browsers and their annotation tracks

samr SAM: Significance Analysis of Microarrays

sandwich Robust Covariance Matrix Estimators

scatterplot3d 3D Scatter Plot

seqLogo Sequence logos for DNA sequence alignments

shapes Statistical shape analysis

ShortRead Base classes and methods for high-throughput short-read sequencing data.

siggenes Multiple testing using SAM and Efron's empirical Bayes approaches

sigPathway Pathway Analysis

simpleaffy Very simple high level analysis of Affymetrix data

sizepower Sample Size and Power Calculation in Micorarray Studies

sma Statistical Microarray Analysis

SMAP A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling

sna Tools for Social Network Analysis

SNPassoc SNPs-based whole genome association studies

SNPchip Classes and Methods for high throughput SNP chip data

snpMatrix The snp.matrix and X.snp.matrix classes

spam SPArse Matrix

SparseM Sparse Linear Algebra

spatial Functions for Kriging and Point Pattern Analysis

splines Regression Spline Functions and Classes

SSOAP Client-side SOAP access for S

statnet Software tools for the Statistical Modeling of Network Data

stats The R Stats Package

stats4 Statistical Functions using S4 Classes

strucchange Testing, Monitoring and Dating Structural Changes

survival Survival analysis, including penalised likelihood.

tcltk Tcl/Tk Interface

tilingArray Analysis of high-density oligonucleotide tiling arrays

tkrplot TK Rplot

tkWidgets R based tk widgets

tools Tools for Package Development

topGO topGO: Enrichment analysis for Gene Ontology

utils The R Utils Package

vsn Variance stabilization and calibration for microarray data

widgetTools Creates an interactive tcltk widget

XML Tools for parsing and generating XML within R and S-Plus.

xtable Export tables to LaTeX or HTML

zoo Z's ordered observations

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
adSplit	Annotation-Driven Clustering
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
amap	Another Multidimensional Analysis Package
annaffy	Annotation tools for Affymetrix biological metadata
annotate	Annotation for microarrays
AnnotationDbi	Annotation Database Interface
ape	Analyses of Phylogenetics and Evolution
aws	Adaptive Weights Smoothing
base	The R Base Package
bayesmix	Bayesian Mixture Models with JAGS
beadarraySNP	Normalization and reporting of Illumina SNP bead arrays
BeadExplorer	QC, normalisation, annotation and exploration of Illumina BeadChip data
Biobase	Biobase: Base functions for Bioconductor
bioDist	Different distance measures
biomaRt	Interface to BioMart databases (e.g. Ensembl, Wormbase and Gramene)
Biostrings	String objects representing biological sequences, and matching algorithms
bitops	Functions for Bitwise operations
boot	Bootstrap R (S-Plus) Functions (Canty)
BSgenome	Infrastructure for Biostrings-based genome data packages
car	Companion to Applied Regression
Category	Category Analysis
caTools	Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
celsius	Retrieve Affymetrix microarray measurements and metadata from Celsius
ChromoViz	Multimodal visualization of gene expression data
class	Functions for Classification
cluster	Cluster Analysis Extended Rousseeuw et al.
coda	Output analysis and diagnostics for MCMC
codetools	Code Analysis Tools for R
combinat	combinatorics utilities
corpcor	Efficient Estimation of Covariance and (Partial) Correlation
cosmo	Supervised detection of conserved motifs in DNA sequences
ctc	Cluster and Tree Conversion.
datasets	The R Datasets Package
DBI	R Database Interface
degreenet	Models for Skewed Count Distributions Relevant to Networks
Design	Design Package
DynDoc	Dynamic document tools
ergm	Fit, Simulate and Diagnose Exponential-Family Models for Networks
exonmap	High level analysis of Affymetrix exon array data
fastICA	FastICA Algorithms to perform ICA and Projection Pursuit
fdrtool	Estimation and Control of (Local) False Discovery Rates
fields	Tools for spatial data
flexclust	Flexible Cluster Algorithms
flexmix	Flexible Mixture Modeling
foreign	Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ...
fork	R functions for handling multiple processes.
gaschYHS	ExpressionSet for response of yeast to heat shock and other environmental stresses
gcrma	Background Adjustment Using Sequence Information
gdata	Various R programming tools for data manipulation
gee	Generalized Estimation Equation solver
GenABEL	genome-wide SNP association analysis
GeneCycle	Identification of Periodically Expressed Genes
genefilter	genefilter: methods for filtering genes from microarray experiments
GeneNet	Modeling and Inferring Gene Networks
geneplotter	Grapics related functions for Bioconductor
genetics	Population Genetics
GeneTS	Microarray Time Series and Network Analysis
GEOquery	Get data from NCBI Gene Expression Omnibus (GEO)
GGBase	infrastructure for genetics of gene expression (c) 2008 VJ Carey
ggplot	An implementation of the Grammar of Graphics in R
ggplot2	An implementation of the Grammar of Graphics
GGtools	software and data for genetical genomics (c) 2006 VJ Carey
GLAD	Gain and Loss Analysis of DNA
GO	A data package containing annotation data for GO
GO.db	A set of annotation maps describing the entire Gene Ontology
goTools	Functions for Gene Ontology database
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
GSEABase	Gene set enrichment data structures and methods
gtools	Various R programming tools
hapassoc	Inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm
haplo.stats	Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
HardyWeinberg	Graphical tests for Hardy-Weinberg equilibrium
hgfocus	Affymetrix Human Genome Focus Array Annotation Data (hgfocus)
hgu95av2	Affymetrix Human Genome U95 Set Annotation Data (hgu95av2)
Hmisc	Harrell Miscellaneous
hopach	Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
hwde	Models and tests for departure from Hardy-Weinberg equilibrium and independence between loci.
ibdreg	Regression Methods for IBD Linkage With Covariates
Icens	NPMLE for Censored and Truncated Data
impute	impute: Imputation for microarray data
IRanges	Low-level containers for storing sets of integer ranges
KEGG	A data package containing annotation data for KEGG
KEGG.db	A set of annotation maps for KEGG
KEGGSOAP	Client-side SOAP access KEGG
KernSmooth	Functions for kernel smoothing for Wand & Jones (1995)
latentnet	Latent position and cluster models for statistical networks
lattice	Lattice Graphics
limma	Linear Models for Microarray Data
lodplot	Plot a genome scan
logicFS	Identification of SNP Interactions
LogicReg	Logic Regression
longitudinal	Analysis of Multiple Time Course Data
lumi	BeadArray Specific Methods for Illumina Microarrays
made4	Multivariate analysis of microarray data using ADE4
mapLD	Linkage Disequilibrium Mapping
maps	Draw Geographical Maps
marray	Exploratory analysis for two-color spotted microarray data
MASS	Main Package of Venables and Ripley's MASS
matchprobes	Basic infrastructure for using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment
Matrix	Sparse and Dense Matrix Classes and Methods
mclust	Model-Based Clustering / Normal Mixture Modeling
methods	Formal Methods and Classes
mgcv	GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL
mgu74av2	Affymetrix Murine Genome U74v2 Annotation Data (mgu74av2)
modeltools	Tools and Classes for Statistical Models
msm	Multi-state Markov and hidden Markov models in continuous time
multcomp	Simultaneous Inference in General Parametric Models
multtest	Resampling-based multiple hypothesis testing
mvtnorm	Multivariate Normal and t Distributions
network	Classes for Relational Data
networksis	Simulate bipartite graphs with fixed marginals through sequential importance sampling
nlme	Linear and Nonlinear Mixed Effects Models
nnet	Feed-forward Neural Networks and Multinomial Log-Linear Models
odesolve	Solvers for Ordinary Differential Equations
oligoClasses	Classes for high-throughput SNP arrays
pcaPP	Robust PCA by Projection Pursuit
pixmap	Bitmap Images (``Pixel Maps'')
plier	Implements the Affymetrix PLIER algorithm
plotrix	Various plotting functions
plyr	Tools for splitting, applying and combining data
prada	Data analysis for cell-based functional assays
preprocessCore	A collection of pre-processing functions
proftools	Profile Output Processing Tools for R
proto	Prototype object-based programming
pvclust	Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling
quadprog	Functions to solve Quadratic Programming Problems.
quantreg	Quantile Regression
quantsmooth	Quantile smoothing and genomic visualization of array data
qvalue	Q-value estimation for false discovery rate control
R2HTML	HTML exportation for R objects
RankProd	Rank Product method for identifying differentially expressed genes with application in meta-analysis
RBGL	An interface to the BOOST graph library
RColorBrewer	ColorBrewer palettes
RCurl	HTTP request interface
Rdonlp2	an R extension library to use Peter Spelluci's DONLP2 from R.
reshape	Flexibly reshape data.
rgl	3D visualization device system (OpenGL)
Rgraphviz	Provides plotting capabilities for R graph objects
Ringo	R Investigation of ChIP-chip Oligoarrays
rJava	Low-level R to Java interface
RMesquite	Wrapper for Mesquite methods in R
RMySQL	R interface to the MySQL database
robustbase	Basic Robust Statistics
ROC	utilities for ROC, with uarray focus
Rolexa	Statistical analysis of Solexa sequencing data
Rolexa.demo	Demo data for the Rolexa package
rpart	Recursive Partitioning
rrcov	Scalable Robust Estimators with High Breakdown Point
RSPerl	The Omegahat interface for R and Perl.
RSQLite	SQLite interface for R
RSvgDevice	An R SVG graphics device.
rtracklayer	R interface to genome browsers and their annotation tracks
samr	SAM: Significance Analysis of Microarrays
sandwich	Robust Covariance Matrix Estimators
scatterplot3d	3D Scatter Plot
seqLogo	Sequence logos for DNA sequence alignments
shapes	Statistical shape analysis
ShortRead	Base classes and methods for high-throughput short-read sequencing data.
siggenes	Multiple testing using SAM and Efron's empirical Bayes approaches
sigPathway	Pathway Analysis
simpleaffy	Very simple high level analysis of Affymetrix data
sizepower	Sample Size and Power Calculation in Micorarray Studies
sma	Statistical Microarray Analysis
SMAP	A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
sna	Tools for Social Network Analysis
SNPassoc	SNPs-based whole genome association studies
SNPchip	Classes and Methods for high throughput SNP chip data
snpMatrix	The snp.matrix and X.snp.matrix classes
spam	SPArse Matrix
SparseM	Sparse Linear Algebra
spatial	Functions for Kriging and Point Pattern Analysis
splines	Regression Spline Functions and Classes
SSOAP	Client-side SOAP access for S
statnet	Software tools for the Statistical Modeling of Network Data
stats	The R Stats Package
stats4	Statistical Functions using S4 Classes
strucchange	Testing, Monitoring and Dating Structural Changes
survival	Survival analysis, including penalised likelihood.
tcltk	Tcl/Tk Interface
tilingArray	Analysis of high-density oligonucleotide tiling arrays
tkrplot	TK Rplot
tkWidgets	R based tk widgets
tools	Tools for Package Development
topGO	topGO: Enrichment analysis for Gene Ontology
utils	The R Utils Package
vsn	Variance stabilization and calibration for microarray data
widgetTools	Creates an interactive tcltk widget
XML	Tools for parsing and generating XML within R and S-Plus.
xtable	Export tables to LaTeX or HTML
zoo	Z's ordered observations