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Package Maintainer Title
ABarray Yongming Andrew Sun Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (AB1700) gene expression data.
aCGH Jane Fridlyand Classes and functions for Array Comparative Genomic Hybridization data.
affxparser Kasper Daniel Hansen Affymetrix File Parsing SDK
affy Rafael A. Irizarry Methods for Affymetrix Oligonucleotide Arrays
affycomp Rafael A. Irizarry Graphics Toolbox for Assessment of Affymetrix Expression Measures
AffyCompatible Martin Morgan Affymetrix GeneChip software compatibility
affyContam V. Carey structured corruption of affymetrix cel file data
AffyExpress Xuejun Arthur Li Affymetrix Quality Assessment and Analysis Tool
affyio Benjamin Milo Bolstad Tools for parsing Affymetrix data files
affylmGUI Keith Satterley GUI for affy analysis using limma package
affyPara Markus Schmidberger Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays
affypdnn Laurent Gautier Probe Dependent Nearest Neighbours (PDNN) for the affy package
affyPLM Ben Bolstad Methods for fitting probe-level models
affyQCReport Craig Parman QC Report Generation for affyBatch objects
AffyTiling Charles G. Danko Easy extraction of individual probes in Affymetrix tiling arrays
Agi4x44PreProcess Pedro Lopez-Romero PreProcessing of Agilent 4x44 array data
altcdfenvs Laurent Gautier alternative CDF environments (aka probeset mappings)
AnnotationDbi Biocore Team c/o BioC user list Annotation Database Interface
apComplex Denise Scholtens Estimate protein complex membership using AP-MS protein data
aroma.light Henrik Bengtsson Light-weight methods for normalization and visualization of microarray data using only basic R data types
ArrayExpress Audrey Kauffmann Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
arrayMvout V. Carey multivariate outlier detection for expression array QA
arrayQuality Agnes Paquet Assessing array quality on spotted arrays
arrayQualityMetrics Audrey Kauffmann Quality metrics on microarray data sets
ArrayTools Arthur Li geneChip Analysis Package
beadarray Mark Dunning Quality assessment and low-level analysis for Illumina BeadArray data
beadarraySNP Jan Oosting Normalization and reporting of Illumina SNP bead arrays
Biobase Biocore Team c/o BioC user list Biobase: Base functions for Bioconductor
BiocCaseStudies Biocore Team c/o BioC user list BiocCaseStudies: Support for the Case Studies Monograph
biocDatasets L. Gautier Synthetic datasets for bioconductor
biocGraph Florian Hahne Graph examples and use cases in Bioinformatics
biocViews Biocore Team c/o BioC user list Categorized views of R package repositories
BioMVCClass Elizabeth Whalen Model-View-Controller (MVC) Classes That Use Biobase
Biostrings H. Pages String objects representing biological sequences, and matching algorithms
BSgenome H. Pages Infrastructure for Biostrings-based genome data packages
BufferedMatrix Benjamin Milo Bolstad A matrix data storage object held in temporary files
BufferedMatrixMethods B. M. Bolstad Microarray Data related methods that utlize BufferedMatrix objects
CALIB Hui Zhao Calibration model for estimating absolute expression levels from microarray data
cellHTS Ligia Bras Analysis of cell-based screens
cellHTS2 Florian Hahne Analysis of cell-based screens - revised version of cellHTS
CGHbase Sjoerd Vosse CGHbase: Base functions and classes for arrayCGH data analysis.
CGHcall Sjoerd Vosse Calling aberrations for array CGH tumor profiles.
CGHregions Sjoerd Vosse Dimension Reduction for Array CGH Data with Minimal Information Loss.
codelink Diego Diez Manipulation of Codelink Bioarrays data.
convert Yee Hwa (Jean) Yang Convert Microarray Data Objects
copa James W. MacDonald Functions to perform cancer outlier profile analysis.
CORREP Dongxiao Zhu Multivariate Correlation Estimator and Statistical Inference Procedures.
cosmoGUI Oliver Bembom GUI for constructing constraint sets used by the cosmo package
crlmm Benilton S Carvalho , Robert Scharpf , Matt Ritchie Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
ctc Antoine Lucas Cluster and Tree Conversion.
dyebias Philip Lijnzaad Methods to correct for gene-specific dye bias
DynDoc Biocore Team c/o BioC user list Dynamic document tools
EBImage Gregoire Pau Image processing and image analysis toolkit for R
ecolitk Laurent Meta-data and tools for E. coli
exonmap Crispin Miller High level analysis of Affymetrix exon array data
explorase Michael Lawrence GUI for exploratory data analysis of systems biology data
externalVector Biocore Team c/o BioC user list Vector objects for R with external storage
flowClust Raphael Gottardo Clustering for Flow Cytometry
flowCore F. Hahne flowCore: Basic structures for flow cytometry data
flowQ F. Hahne Qualitiy control for flow cytometry
flowUtils Nishant Gopalakrishnan Utilities for flow cytometry
flowViz Florian Hahne Visualization for flow cytometry
gaggle Dan Tenenbaum Broadcast data between R and other bioinformatics programs
gcrma Z. Wu Background Adjustment Using Sequence Information
genArise IFC Development Team Microarray Analysis tool
gene2pathway Holger Froehlich Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures
geneplotter Biocore Team c/o BioC user list Graphics related functions for Bioconductor
GeneRegionScan Lasse Folkersen GeneRegionScan
GeneSpring Thon de Boer GeneSpring R Integration Functions
GeneTraffic Daniel Iordan GeneTraffic R Integration Functions
GenomeGraphs Steffen Durinck Plotting genomic information from Ensembl
genomeIntervals Julien Gagneur Operations on genomic intervals
GEOmetadb Jack Zhu A compilation of metadata from NCBI GEO
GEOquery Sean Davis Get data from NCBI Gene Expression Omnibus (GEO)
goTools Agnes Paquet Functions for Gene Ontology database
graph Robert Gentleman graph: A package to handle graph data structures
GraphAlignment Joern P. Meier GraphAlignment
GraphAT Thomas LaFramboise Graph Theoretic Association Tests
GSEABase Biocore Team c/o BioC user list Gene set enrichment data structures and methods
Heatplus Alexander Ploner A heat map displaying covariates and coloring clusters
HELP Reid F. Thompson Tools for HELP data analysis
hexbin Nicholas Lewin-Koh Hexagonal Binning Routines
HilbertVis Simon Anders Hilbert curve visualization
HilbertVisGUI Simon Anders HilbertVisGUI
hypergraph Robert Gentleman A package providing hypergraph data structures
Icens Biocore Team c/o BioC user list NPMLE for Censored and Truncated Data
idiogram Karl J. Dykema idiogram
IRanges Biocore Team c/o BioC user list Infrastructure for manipulating intervals on sequences
KCsmart Jorma de Ronde Multi sample aCGH analysis package using kernel convolution
KEGGgraph Jitao David Zhang KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
keggorth VJ Carey graph support for KO, KEGG Orthology
limma Gordon Smyth Linear Models for Microarray Data
limmaGUI Keith Satterley GUI for limma package
LMGene John Tillinghast LMGene Software for Date Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
lumi Pan Du BeadArray Specific Methods for Illumina Microarrays
macat Joern Toedling MicroArray Chromosome Analysis Tool
maCorrPlot Alexander Ploner Visualize artificial correlation in microarray data
maDB Johannes Rainer Microarray database and utility functions for microarray data analysis.
maigesPack Gustavo H. Esteves Functions to handle cDNA microarray data, including several methods of data analysis
makecdfenv James W. MacDonald CDF Environment Maker
makePlatformDesign Benilton Carvalho Platform Design Package
MANOR Pierre Neuvial CGH Micro-Array NORmalization
marray Yee Hwa (Jean) Yang Exploratory analysis for two-color spotted microarray data
MergeMaid Xiaogang Zhong Merge Maid
Mfuzz Matthias Futschik Soft clustering of time series gene expression data
microRNA Robert Gentleman Data and functions for dealing with microRNAs
minet Patrick E. Meyer Mutual Information Network Inference
multiscan Mizanur Khondoker R package for combining multiple scans
MVCClass Elizabeth Whalen Model-View-Controller (MVC) Classes
nem Christian Bender Nested Effects Models to reconstruct phenotypic hierarchies
nnNorm Adi Laurentiu Tarca Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
oligo Benilton Carvalho Tools for low-level analysis of oligonucleotide arrays.
oligoClasses Benilton Carvalho Classes for high-throughput SNP arrays
OLIN Matthias Futschik Optimized local intensity-dependent normalisation of two-color microarrays
OLINgui Matthias Futschik Graphical user interface for OLIN
oneChannelGUI Raffaele A Calogero This package extends the capabilities of affylmGUI graphical interface. Affymetrix 3' IVT, gene an exon arrays are actually implemented togheter with Illumina, GEO matrix series files and tab delimited files.
ontoTools Vince Carey graphs and sparse matrices for working with ontologies; formal objects for nomenclatures with provenance management
pathRender Li Long Render molecular pathways
PCpheno Nolwenn Le Meur Phenotypes and cellular organizational units
pdInfoBuilder Benilton Carvalho Platform Design Information Package Builder
pgUtils Johannes Rainer Utility functions for PostgreSQL databases
pkgDepTools Seth Falcon Package Dependency Tools
ppiStats Tony Chiang Protein-Protein Interaction Statistical Package
prada Florian Hahne Data analysis for cell-based functional assays
preprocessCore Benjamin Milo Bolstad A collection of pre-processing functions
puma Richard Pearson Propagating Uncertainty in Microarray Analysis
qpcrNorm Jessica Mar Data-driven normalization strategies for high-throughput qPCR data.
qpgraph Robert Castelo Reverse engineering of molecular regulatory networks with qp-graphs
quantsmooth Jan Oosting Quantile smoothing and genomic visualization of array data
rama Raphael Gottardo Robust Analysis of MicroArrays
RBGL Li Long An interface to the BOOST graph library
Rdbi Jianhua Zhang Generic database methods
RdbiPgSQL Jianhua Zhang PostgreSQL access
reb Karl J. Dykema Regional Expression Biases
RefPlus Kai-Ming Chang A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
rflowcyt N. LeMeur Statistical tools and data structures for analytic flow cytometry
Rgraphviz Kasper Hansen Provides plotting capabilities for R graph objects
rHVDM Martino Barenco Hidden Variable Dynamic Modeling
Ringo J. Toedling R Investigation of ChIP-chip Oligoarrays
Rintact Tony Chiang Interface to EBI Intact protein interaction data base
rMAT Arnaud Droit and Raphael Gottardo R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
RNAither Nora Rieber Statistical analysis of high-throughput RNAi screens
RpsiXML Jitao David Zhang R interface to PSI-MI 2.5 files
Rredland VJ Carey interface to redland RDF utilities
rsbml Michael Lawrence R support for SBML, using libsbml
rtracklayer Michael Lawrence R interface to genome browsers and their annotation tracks
Ruuid Biocore Team c/o BioC user list Ruuid: Provides Universally Unique ID values
RWebServices Martin Morgan Expose R functions as web services through Java/Axis/Apache
SAGx Per Broberg, Statistical Analysis of the GeneChip
SBMLR Tomas Radivoyevitch SBML-R Interface and Analysis Tools
ScISI Tony Chiang In Silico Interactome
ShortRead Biocore Team c/o BioC user list Base classes and methods for high-throughput short-read sequencing data.
SIM Maarten van Iterson Integrated Analysis of gene expression and copynumber data
simpleaffy Crispin Miller Very simple high level analysis of Affymetrix data
simulatorAPMS Tony Chiang Computationally simulates the AP-MS technology.
SLGI Nolwenn Le Meur Synthetic Lethal Genetic Interaction
snapCGH John Marioni Segmentation, normalisation and processing of aCGH data.
SNPchip Robert Scharpf Classes and Methods for high throughput SNP chip data
SPIA Adi Laurentiu Tarca Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
spikeLI Enrico Carlon Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
splicegear Laurent Gautier splicegear
spotSegmentation Chris Fraley Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
stepNorm Yuanyuan Xiao Stepwise normalization functions for cDNA microarrays
TargetSearch Alvaro Cuadros-Inostroza A package for the analysis of GC-MS metabolite profiling data.
tilingArray Zhenyu Xu Transcript mapping with high-density oligonucleotide tiling arrays
tkWidgets J. Zhang R based tk widgets
topGO Adrian Alexa topGO: Enrichment analysis for Gene Ontology
TypeInfo Duncan Temple Lang Optional Type Specification Prototype
VanillaICE Robert Scharpf A Hidden Markov Model for high throughput genotyping arrays
vsn Wolfgang Huber Variance stabilization and calibration for microarray data
weaver Seth Falcon Tools and extensions for processing Sweave documents
webbioc Colin A. Smith Bioconductor Web Interface
widgetTools Jianhua Zhang Creates an interactive tcltk widget
xmapbridge Tim Yates Export plotting files to the xmapBridge for visualisation in X:Map
xps Christian Stratowa Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
yaqcaffy Laurent Gatto Affymetrix expression data quality control and reproducibility analysis