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Package Maintainer Title
aCGH Peter Dimitrov Classes and functions for Array Comparative Genomic Hybridization data.
ADaCGH2 Ramon Diaz-Uriarte Analysis of data from aCGH experiments using parallel computing and ff objects
affycoretools James W. MacDonald Functions useful for those doing repetitive analyses with Affymetrix GeneChips.
AffyExpress Xuejun Arthur Li Affymetrix Quality Assessment and Analysis Tool
affylmGUI Keith Satterley GUI for affy analysis using limma package
AgiMicroRna Pedro Lopez-Romero Processing and Differential Expression Analysis of Agilent microRNA chips
altcdfenvs Laurent Gautier alternative CDF environments (aka probeset mappings)
ArrayTools Arthur Li geneChip Analysis Package
attract Jessica Mar Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
BAC Raphael Gottardo Bayesian Analysis of Chip-chip experiment
baySeq Thomas J. Hardcastle Empirical Bayesian analysis of patterns of differential expression in count data
beadarraySNP Jan Oosting Normalization and reporting of Illumina SNP bead arrays
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
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
BSgenome H. Pages Infrastructure for Biostrings-based genome data packages
cellHTS Ligia Bras Analysis of cell-based screens
cellHTS2 Florian Hahne Analysis of cell-based screens - revised version of cellHTS
CGEN William Wheeler An R package for analysis of case-control studies in genetic epidemiology
CGHbase Sjoerd Vosse CGHbase: Base functions and classes for arrayCGH data analysis.
cghMCR J. Zhang Find chromosome regions showing common gains/losses
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.
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.
CNVtools Chris Barnes A package to test genetic association with CNV data
CoGAPS Elana J. Fertig , Michael F. Ochs Coordinated Gene Activity in Pattern Sets
copa James W. MacDonald Functions to perform cancer outlier profile analysis.
coRNAi Elin Axelsson Analysis of co-knock-down RNAi data
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
daMA Jobst Landgrebe Efficient design and analysis of factorial two-colour microarray data
ddCt Jitao David Zhang The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
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
EBarrays Ming Yuan Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
edd Vince Carey expression density diagnostics
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)
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
flowCore F. Hahne flowCore: Basic structures for flow cytometry data
flowFP Herb Holyst Fingerprinting for Flow Cytometry
flowQ F. Hahne Qualitiy control for flow cytometry
flowStats Florian Hahne and Chao-Jen Wong Statistical methods for the analysis of flow cytometry data
flowUtils Nishant Gopalakrishnan Utilities for flow cytometry
flowViz Florian Hahne Visualization for flow cytometry
gaga David Rossell GaGa hierarchical model for microarray data analysis
gage Weijun Luo Generally Applicable Gene-set Enrichment for Pathway Analysis
GeneGA Zhenpeng Li Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
GeneRegionScan Lasse Folkersen GeneRegionScan
GeneSelectMMD Weiliang Qiu Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions
GeneSelector Martin Slawski Stability and Aggregation of ranked gene lists
GGBase Vince Carey infrastructure for genetics of gene expression (c) 2008 VJ Carey
GGtools Vince Carey software and data for genetics of gene expression (c) 2006 VJ Carey
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
goseq Matthew Young Gene Ontology analyser for RNA-seq and other length biased data
GSRI Julian Gehring Gene Set Regulation Index
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
HTSanalyzeR Xin Wang Gene set over-representation, enrichment and network analyses for high-throughput screens
imageHTS Gregoire Pau Analysis of high-throughput microscopy-based screens
IsoGeneGUI Setia Pramana A graphical user interface to conduct a dose-response analysis of microarray data
ITALICS Guillem Rigaill ITALICS
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
LiquidAssociation Yen-Yi Ho LiquidAssociation
LMGene Blythe Durbin-Johnson LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
logicFS Holger Schwender Identification of SNP Interactions
logitT Tobias Guennel logit-t Package
LPE Nitin Jain Methods for analyzing microarray data using Local Pooled Error (LPE) method
lumi Pan Du BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
maanova Keith Sheppard Tools for analyzing Micro Array experiments
macat Joern Toedling MicroArray Chromosome Analysis Tool
maigesPack Gustavo H. Esteves Functions to handle cDNA microarray data, including several methods of data analysis
MANOR Pierre Neuvial CGH Micro-Array NORmalization
maSigPro Ana Conesa Significant Gene Expression Profile Differences in Time Course Microarray Data
MassArray Reid F. Thompson Analytical Tools for MassArray Data
mBPCR P.M.V. Rancoita Bayesian Piecewise Constant Regression for DNA copy number estimation
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
methVisual Arie Zackay Methods for visualization and statistics on DNA methylation data
methylumi Sean Davis Handle Illumina methylation data
miRNApath James M. Ward miRNApath: Pathway Enrichment for miRNA Expression Data
MotIV Eloi Mercier , Raphael Gottardo Motif Identification and Validation
Mulcom Claudio Isella Calculates MulCom test
multtest Katherine S. Pollard Resampling-based multiple hypothesis testing
netresponse Leo Lahti NetResponse: functional network analysis
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.
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
pcot2 Sarah Song Principal Coordinates and Hotelling's T-Square method
pickgene Brian S. Yandell Adaptive Gene Picking for Microarray Expression Data Analysis
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.
prada Florian Hahne Data analysis for cell-based functional assays
PROMISE Xueyuan Cao PRojection Onto the Most Interesting Statistical Evidence
puma Richard Pearson , Li Zhang 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
RankProd Fangxin Hong Rank Product method for identifying differentially expressed genes with application in meta-analysis
RBioinf Robert Gentleman RBioinf
reb Karl J. Dykema Regional Expression Biases
rflowcyt N. LeMeur Statistical tools and data structures for analytic flow cytometry
rGADEM Arnaud Droit de novo motif discovery
rHVDM Martino Barenco Hidden Variable Dynamic Modeling
RLMM Nusrat Rabbee A Genotype Calling Algorithm for Affymetrix SNP Arrays
RmiR Francesco Favero Package to work with miRNAs and miRNA targets with R
RNAither Nora Rieber Statistical analysis of high-throughput RNAi screens
rnaSeqMap Michal Okoniewski rnaSeq analyses using xmapcore database
ROC Vince Carey utilities for ROC, with uarray focus
RPA Leo Lahti RPA: probe reliability and differential gene expression analysis
RTCA Jitao David Zhang Open-source toolkit to analyse data from xCELLigence System (RTCA) by Roche
RTools4TB Aurelie Bergon Data mining of public microarray data through connections to the TranscriptomeBrowser database.
SAGx Per Broberg, Statistical Analysis of the GeneChip
siggenes Holger Schwender Multiple testing using SAM and Efron's empirical Bayes approaches
sigPathway Weil Lai Pathway Analysis
simpleaffy Crispin Miller Very simple high level analysis of Affymetrix data
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.
SNPchip Robert Scharpf Classes and Methods for high throughput SNP chip data
snpMatrix David Clayton The snp.matrix and X.snp.matrix classes
SpeCond Florence Cavalli Condition specific detection from expression data
splicegear Laurent Gautier splicegear
sscore Richard Kennedy S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
ssize Gregory R. Warnes Estimate Microarray Sample Size
Starr Benedikt Zacher Simple tiling array analysis of Affymetrix ChIP-chip data
tigre Antti Honkela Transcription factor Inference through Gaussian process Reconstruction of Expression
timecourse Yu Chuan Tai Statistical Analysis for Developmental Microarray Time Course Data
twilight Stefanie Scheid Estimation of local false discovery rate
VanillaICE Robert Scharpf A Hidden Markov Model for high throughput genotyping arrays
webbioc Colin A. Smith Bioconductor Web Interface
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