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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.
ADaCGH2 Ramon Diaz-Uriarte Analysis of data from aCGH experiments using parallel computing and ff objects
adSplit Claudio Lottaz Annotation-Driven Clustering
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
affycoretools James W. MacDonald Functions useful for those doing repetitive analyses with Affymetrix GeneChips.
AffyExpress Xuejun Arthur Li Affymetrix Quality Assessment and Analysis Tool
affyILM Myriam Kroll and Fabrice Berger Linear Model of background subtraction and the Langmuir isotherm
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
AgiMicroRna Pedro Lopez-Romero Processing and Differential Expression Analysis of Agilent microRNA chips
altcdfenvs Laurent Gautier alternative CDF environments (aka probeset mappings)
annaffy Colin A. Smith Annotation tools for Affymetrix biological metadata
annotationTools Alexandre Kuhn Annotate microarrays and perform cross-species gene expression analyses using flat file databases.
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
BAC Raphael Gottardo Bayesian Analysis of Chip-chip experiment
BayesPeak Jonathan Cairns Bayesian Analysis of ChIP-seq Data
baySeq Thomas J. Hardcastle Empirical Bayesian analysis of patterns of differential expression in count data
beadarray Mark Dunning Quality assessment and low-level analysis for Illumina BeadArray data
beadarraySNP Jan Oosting Normalization and reporting of Illumina SNP bead arrays
BeadDataPackR Mike Smith Compression of Illumina BeadArray data
betr Martin Aryee Identify differentially expressed genes in microarray time-course data
BGmix Alex Lewin Bayesian models for differential gene expression
bgx Ernest Turro Bayesian Gene eXpression
BHC Rich Savage Bayesian Hierarchical Clustering
BicARE Pierre Gestraud Biclustering Analysis and Results Exploration
BioNet Marcus Dittrich Routines for the functional analysis of biological networks
bridge Raphael Gottardo Bayesian Robust Inference for Differential Gene Expression
CALIB Hui Zhao Calibration model for estimating absolute expression levels from microarray data
CAMERA Carsten Kuhl Collection of annotation related methods for mass spectrometry data
CGHbase Sjoerd Vosse CGHbase: Base functions and classes for arrayCGH data analysis.
CGHcall Mark van de Wiel Calling aberrations for array CGH tumor profiles.
cghMCR J. Zhang Find chromosome regions showing common gains/losses
CGHnormaliter Bart P.P. van Houte Normalization of array CGH data with imbalanced aberrations.
CGHregions Sjoerd Vosse Dimension Reduction for Array CGH Data with Minimal Information Loss.
charm Martin Aryee Analysis of DNA methylation data from CHARM microarrays
ChemmineR ChemmineR Team Analysis of Small Molecule and Screening Data
ChIPpeakAnno Lihua Julie Zhu Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.
chipseq Biocore Team c/o BioC user list chipseq: A package for analyzing chipseq data
ChIPseqR Peter Humburg Identifying Protein Binding Sites in High-Throughput Sequencing Data
ChIPsim Peter Humburg Simulation of ChIP-seq experiments
clippda Stephen Nyangoma A package for the clinical proteomic profiling data analysis
CNTools J. Zhang Convert segment data into a region by sample matrix to allow for other high level computational analyses.
codelink Diego Diez Manipulation of Codelink Bioarrays data.
CoGAPS Elana J. Fertig , Michael F. Ochs Coordinated Gene Activity in Pattern Sets
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.
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.
CSAR Jose M Muino Statistical tools for the analysis of ChIP-seq data
ctc Antoine Lucas Cluster and Tree Conversion.
cycle Matthias Futschik Significance of periodic expression pattern in time-series data
daMA Jobst Landgrebe Efficient design and analysis of factorial two-colour microarray data
DEDS Yuanyuan Xiao Differential Expression via Distance Summary for Microarray Data
DEGraph Laurent Jacob Two-sample tests on a graph
DEGseq Likun Wang Identify Differentially Expressed Genes from RNA-seq data
DESeq Simon Anders Digital gene expresion analysis based on the negative binomial distribution
DFP Rodrigo Alvarez-Glez Gene Selection
diffGeneAnalysis Choudary Jagarlamudi Performs differential gene expression Analysis
DNAcopy Venkatraman E. Seshan DNA copy number data analysis
dualKS Eric J. Kort Dual KS Discriminant Analysis and Classification
dyebias Philip Lijnzaad The GASSCO method for correcting for slide-dependent gene-specific dye bias
edgeR Mark Robinson , Davis McCarthy , Gordon Smyth Empirical analysis of digital gene expression data in R
eisa Gabor Csardi Expression data analysis via the Iterative Signature Algorithm
exonmap Crispin Miller High level analysis of Affymetrix exon array data (DEPRECATED please use xmapcore)
explorase Michael Lawrence GUI for exploratory data analysis of systems biology data
ExpressionView Gabor Csardi Visualize biclusters identified in gene expression data
fabia Sepp Hochreiter FABIA: Factor Analysis for Bicluster Acquisition
factDesign Denise Scholtens Factorial designed microarray experiment analysis
farms Djork-Arne Clevert FARMS - Factor Analysis for Robust Microarray Summarization
fdrame Effi Kenigsberg FDR adjustments of Microarray Experiments (FDR-AME)
flagme Mark Robinson Analysis of Metabolomics GC/MS Data
flowClust Raphael Gottardo Clustering for Flow Cytometry
flowCore F. Hahne flowCore: Basic structures for flow cytometry data
flowFlowJo John J. Gosink Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm.
flowFP Herb Holyst Fingerprinting for Flow Cytometry
flowMeans Nima Aghaeepour Non-parametric Flow Cytometry Data Gating
flowMerge Greg Finak Cluster Merging for Flow Cytometry Data
flowQ F. Hahne Qualitiy control for flow cytometry
flowStats Florian Hahne and Chao-Jen Wong Statistical methods for the analysis of flow cytometry data
flowTrans Greg Finak Parameter Optimization for Flow Cytometry Data Transformation
flowUtils Nishant Gopalakrishnan Utilities for flow cytometry
flowViz Florian Hahne Visualization for flow cytometry
frma Matthew N. McCall Frozen RMA and Barcode
frmaTools Matthew N. McCall Frozen RMA Tools
gage Weijun Luo Generally Applicable Gene-set Enrichment for Pathway Analysis
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
genefilter Biocore Team c/o BioC user list genefilter: methods for filtering genes from microarray experiments
geneRecommender Greg Hather A gene recommender algorithm to identify genes coexpressed with a query set of genes
GeneRegionScan Lasse Folkersen GeneRegionScan
GeneTraffic Daniel Iordan GeneTraffic R Integration Functions
genoCN Wei Sun genotyping and copy number study tools
GenomeGraphs Steffen Durinck Plotting genomic information from Ensembl
GenomicFeatures Biocore Team c/o BioC user list Tools for making and manipulating transcript centric annotations
GenomicRanges Biocore Team c/o BioC user list Representation and manipulation of genomic intervals
GEOquery Sean Davis Get data from NCBI Gene Expression Omnibus (GEO)
GEOsubmission Alexandre Kuhn Prepares microarray data for submission to GEO
girafe J. Toedling Genome Intervals and Read Alignments for Functional Exploration
GLAD Philippe Hupe Gain and Loss Analysis of DNA
GlobalAncova R. Meister Calculates a global test for differential gene expression between groups
globaltest Jelle Goeman Testing groups of covariates/features for association with a response variable, with applications to gene set testing
goProfiles Alex Sanchez goProfiles: an R package for the statistical analysis of functional profiles
goseq Matthew Young Gene Ontology analyser for RNA-seq and other length biased data
goTools Agnes Paquet Functions for Gene Ontology database
gpls Biocore Team c/o BioC user list Classification using generalized partial least squares
GSEAlm Assaf Oron Linear Model Toolset for Gene Set Enrichment Analysis
GSRI Julian Gehring Gene Set Regulation Index
Harshlight Maurizio Pellegrino A "corrective make-up" program for microarray chips
Heatplus Alexander Ploner A heat map displaying covariates and coloring clusters
HELP Reid F. Thompson Tools for HELP data analysis
HEM HyungJun Cho Heterogeneous error model for identification of differentially expressed genes under multiple conditions
HTqPCR Heidi Dvinge Automated analysis of high-throughput qPCR data
iChip Qianxing Mo Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
impute Balasubramanian Narasimhan impute: Imputation for microarray data
IsoGeneGUI Setia Pramana A graphical user interface to conduct a dose-response analysis of microarray data
ITALICS Guillem Rigaill ITALICS
iterativeBMA Ka Yee Yeung The Iterative Bayesian Model Averaging (BMA) algorithm
iterativeBMAsurv Ka Yee Yeung The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis
KCsmart Jorma de Ronde Multi sample aCGH analysis package using kernel convolution
lapmix Yann Ruffieux Laplace Mixture Model in Microarray Experiments
les Julian Gehring Identifying Loci of Enhanced Significance in Tiling Microarray Data
limma Gordon Smyth Linear Models for Microarray Data
limmaGUI Keith Satterley GUI for limma package
LMGene Blythe Durbin-Johnson LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
logitT Tobias Guennel logit-t Package
LPE Nitin Jain Methods for analyzing microarray data using Local Pooled Error (LPE) method
LPEadj Carl Murie A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.
lumi Pan Du BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
LVSmiRNA Stefano Calza LVS normalization for Agilent miRNA data
maanova Keith Sheppard Tools for analyzing Micro Array experiments
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
maSigPro Ana Conesa Significant Gene Expression Profile Differences in Time Course Microarray Data
MassArray Reid F. Thompson Analytical Tools for MassArray Data
MassSpecWavelet Pan Du Mass spectrum processing by wavelet-based algorithms
MBCB Jeff Allen MBCB (Model-based Background Correction for Beadarray)
mBPCR P.M.V. Rancoita Bayesian Piecewise Constant Regression for DNA copy number estimation
MEDIPS Lukas Chavez MeDIP-Seq data analysis
MEDME Mattia Pelizzola Modelling Experimental Data from MeDIP Enrichment
MergeMaid Xiaogang Zhong Merge Maid
metaArray Hyungwon Choi Integration of Microarray Data for Meta-analysis
metahdep John R. Stevens Hierarchical Dependence in Meta-Analysis
methylumi Sean Davis Handle Illumina methylation data
Mfuzz Matthias Futschik Soft clustering of time series gene expression data
MiChip Jonathon Blake MiChip Parsing and Summarizing Functions
minet Patrick E. Meyer Mutual Information NETworks
MiPP Sukwoo Kim Misclassification Penalized Posterior Classification
MotIV Eloi Mercier , Raphael Gottardo Motif Identification and Validation
Mulcom Claudio Isella Calculates MulCom test
multiscan Mizanur Khondoker R package for combining multiple scans
multtest Katherine S. Pollard Resampling-based multiple hypothesis testing
nem Christian Bender Nested Effects Models to reconstruct phenotypic hierarchies
netresponse Leo Lahti NetResponse: functional network analysis
nnNorm Adi Laurentiu Tarca Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
nudge N. Dean Normal Uniform Differential Gene Expression detection
OCplus Alexander Ploner Operating characteristics plus sample size and local fdr for microarray experiments
oligo Benilton Carvalho Preprocessing tools for oligonucleotide 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. Next Generation Sequencing secondary analysis for ncRNA quantification is also available.
OrderedList Claudio Lottaz Similarities of Ordered Gene Lists
OutlierD Sukwoo Kim Outlier detection using quantile regression on the M-A scatterplots of high-throughput data
pamr Rob Tibshirani Pam: prediction analysis for microarrays
pcot2 Sarah Song Principal Coordinates and Hotelling's T-Square method
PGSEA Karl Dykema Parametric Gene Set Enrichment Analysis
pickgene Brian S. Yandell Adaptive Gene Picking for Microarray Expression Data Analysis
PICS Arnaud Droit , Xuekui Zhang , Raphael Gottardo Probabilistic inference of ChIP-seq
pint Olli-Pekka Huovilainen Pairwise INTegration of functional genomics data
plateCore Errol Strain Statistical tools and data structures for plate-based flow cytometry
plgem Norman Pavelka Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
PLPE Soo-heang Eo Local Pooled Error Test for Differential Expression with Paired High-throughput Data
plw Magnus Astrand Probe level Locally moderated Weighted t-tests.
PROcess Xiaochun Li Ciphergen SELDI-TOF Processing
PROMISE Xueyuan Cao PRojection Onto the Most Interesting Statistical Evidence
puma Richard Pearson , Li Zhang Propagating Uncertainty in Microarray Analysis
qpgraph Robert Castelo Reverse engineering of molecular regulatory networks with qp-graphs
R453Plus1Toolbox H-U Klein A package for importing and analyzing data from Roche's Genome Sequencer System.
rama Raphael Gottardo Robust Analysis of MicroArrays
RBioinf Robert Gentleman RBioinf
rbsurv Soo-heang Eo Robust likelihood-based survival modeling with microarray data
Rdisop Steffen Neumann Decomposition of Isotopic Patterns
RDRToolbox Christoph Bartenhagen A package for nonlinear dimension reduction with Isomap and LLE.
reb Karl J. Dykema Regional Expression Biases
RefPlus Kai-Ming Chang A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
Resourcerer Jianhua Zhang Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge.
rGADEM Arnaud Droit de novo motif discovery
rHVDM Martino Barenco Hidden Variable Dynamic Modeling
Ringo J. Toedling R Investigation of ChIP-chip Oligoarrays
RLMM Nusrat Rabbee A Genotype Calling Algorithm for Affymetrix SNP Arrays
RMAGEML Steffen Durinck Handling MAGEML documents
Rmagpie Camille Maumet MicroArray Gene-expression-based Program In Error rate estimation
rMAT Arnaud Droit and Raphael Gottardo R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
RmiR Francesco Favero Package to work with miRNAs and miRNA targets with R
rnaSeqMap Michal Okoniewski rnaSeq analyses using xmapcore database
Rolexa Jacques Rougemont Statistical analysis of Solexa sequencing data
RPA Leo Lahti RPA: probe reliability and differential gene expression analysis
Rsamtools Biocore Team c/o BioC user list Import aligned BAM file format sequences into R / Bioconductor
RTools4TB Aurelie Bergon Data mining of public microarray data through connections to the TranscriptomeBrowser database.
sagenhaft Tim Beissbarth Collection of functions for reading and comparing SAGE libraries
SAGx Per Broberg, Statistical Analysis of the GeneChip
SamSPECTRAL Habil Zare Identifies cell population in flow cytometry data.
segmentSeq Thomas J. Hardcastle Methods for identifying small RNA loci from high-throughput sequencing data
ShortRead Biocore Team c/o BioC user list Classes and methods for high-throughput short-read sequencing data.
siggenes Holger Schwender Multiple testing using SAM and Efron's empirical Bayes approaches
SIM Maarten van Iterson Integrated Analysis on two human genomic datasets
simpleaffy Crispin Miller Very simple high level analysis of Affymetrix data
simulatorAPMS Tony Chiang Computationally simulates the AP-MS technology.
sizepower Weiliang Qiu Sample Size and Power Calculation in Micorarray Studies
SMAP Robin Andersson A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
snapCGH John Marioni Segmentation, normalisation and processing of aCGH data.
snpMatrix David Clayton The snp.matrix and X.snp.matrix classes
SpeCond Florence Cavalli Condition specific detection from expression 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
spkTools Matthew N McCall Methods for Spike-in Arrays
splots Wolfgang Huber Visualization of high-throughput assays in microtitre plate or slide format
spotSegmentation Chris Fraley Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
SRAdb Jack Zhu A compilation of metadata from NCBI SRA and tools
ssize Gregory R. Warnes Estimate Microarray Sample Size
SSPA Maarten van Iterson Sample Size and Power Analysis for Microarray Data
Starr Benedikt Zacher Simple tiling array analysis of Affymetrix ChIP-chip data
stepNorm Yuanyuan Xiao Stepwise normalization functions for cDNA microarrays
TargetSearch Alvaro Cuadros-Inostroza A package for the analysis of GC-MS metabolite profiling data.
tigre Antti Honkela Transcription factor Inference through Gaussian process Reconstruction of Expression
tilingArray Zhenyu Xu Transcript mapping with high-density oligonucleotide tiling arrays
timecourse Yu Chuan Tai Statistical Analysis for Developmental Microarray Time Course Data
topGO Adrian Alexa topGO: Enrichment analysis for Gene Ontology
tspair Jeffrey T. Leek Top Scoring Pairs for Microarray Classification
twilight Stefanie Scheid Estimation of local false discovery rate
vsn Wolfgang Huber Variance stabilization and calibration for microarray data
webbioc Colin A. Smith Bioconductor Web Interface
xcms Colin A. Smith LC/MS and GC/MS Data Analysis
XDE Robert Scharpf XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
xmapcore Tim Yates Core access to the xmap database (installed separately)
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