Bioconductor Software Packages

Bioconductor version: 3.1

Package	Maintainer	Title
a4	Tobias Verbeke, Willem Ligtenberg	Automated Affymetrix Array Analysis Umbrella Package
a4Base	Tobias Verbeke, Willem Ligtenberg	Automated Affymetrix Array Analysis Base Package
a4Classif	Tobias Verbeke, Willem Ligtenberg	Automated Affymetrix Array Analysis Classification Package
a4Core	Tobias Verbeke, Willem Ligtenberg	Automated Affymetrix Array Analysis Core Package
a4Preproc	Tobias Verbeke, Willem Ligtenberg	Automated Affymetrix Array Analysis Preprocessing Package
a4Reporting	Tobias Verbeke, Willem Ligtenberg	Automated Affymetrix Array Analysis Reporting Package
ABarray	Yongming Andrew Sun	Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.
ABSSeq	Wentao Yang	ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
aCGH	Peter Dimitrov	Classes and functions for Array Comparative Genomic Hybridization data.
ACME	Sean Davis	Algorithms for Calculating Microarray Enrichment (ACME)
ADaCGH2	Ramon Diaz-Uriarte	Analysis of big data from aCGH experiments using parallel computing and ff objects
adSplit	Claudio Lottaz	Annotation-Driven Clustering
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
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
AffyRNADegradation	Mario Fasold	Analyze and correct probe positional bias in microarray data due to RNA degradation
AffyTiling	Charles G. Danko	Easy extraction of individual probes in Affymetrix tiling arrays
AGDEX	Cuilan lani Gao	Agreement of Differential Expression Analysis
agilp	Benny Chain	Agilent expression array processing package
AgiMicroRna	Pedro Lopez-Romero	Processing and Differential Expression Analysis of Agilent microRNA chips
AIMS	Eric R Paquet	AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
ALDEx2	Greg Gloor	Analysis of differential abundance taking sample variation into account
AllelicImbalance	Jesper R Gadin	Investigates allele specific expression
alsace	Ron Wehrens	ALS for the Automatic Chemical Exploration of mixtures
altcdfenvs	Laurent Gautier	alternative CDF environments (aka probeset mappings)
ampliQueso	Michal Okoniewski	Analysis of amplicon enrichment panels
AnalysisPageServer	Brad Friedman	A framework for sharing interactive data and plots from R through the web.
annaffy	Colin A. Smith	Annotation tools for Affymetrix biological metadata
annmap	Chris Wirth	Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
annotate	Bioconductor Package Maintainer	Annotation for microarrays
AnnotationDbi	Bioconductor Package Maintainer	Annotation Database Interface
AnnotationForge	Bioconductor Package Maintainer	Code for Building Annotation Database Packages
AnnotationFuncs	Stefan McKinnon Edwards	Annotation translation functions
AnnotationHub	Bioconductor Package Maintainer	Client to access AnnotationHub resources
annotationTools	Alexandre Kuhn	Annotate microarrays and perform cross-species gene expression analyses using flat file databases.
anota	Ola Larsson	ANalysis Of Translational Activity (ANOTA).
antiProfiles	Hector Corrada Bravo	Implementation of gene expression anti-profiles
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	Ugis Sarkans	Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
ArrayExpressHTS	Angela Goncalves, Andrew Tikhonov	ArrayExpress High Throughput Sequencing Processing Pipeline
arrayMvout	V. Carey	multivariate outlier detection for expression array QA
arrayQuality	Agnes Paquet	Assessing array quality on spotted arrays
arrayQualityMetrics	Audrey Kauffmann	Quality metrics report for microarray data sets
ArrayTools	Arthur Li	geneChip Analysis Package
ArrayTV	Eitan Halper-Stromberg	Implementation of wave correction for arrays
ARRmNormalization	Jean-Philippe Fortin	Adaptive Robust Regression normalization for Illumina methylation data
ASEB	Likun Wang	Predict Acetylated Lysine Sites
ASGSCA	Hela Romdhani	Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models
ASSET	William Wheeler	An R package for subset-based association analysis of heterogeneous traits and subtypes
ASSIGN	Ying Shen	Adaptive Signature Selection and InteGratioN (ASSIGN)
AtlasRDF	James Malone	Gene Expression Atlas query and gene set enrichment 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
BADER	Andreas Neudecker	Bayesian Analysis of Differential Expression in RNA Sequencing Data
BAGS	Alejandro Quiroz-Zarate	A Bayesian Approach for Geneset Selection
ballgown	Alyssa Frazee	Flexible, isoform-level differential expression analysis
bamsignals	Alessandro Mammana	Extract read count signals from bam files
BaseSpaceR	Jared O'Connell	R SDK for BaseSpace RESTful API
Basic4Cseq	Carolin Walter	Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
BayesPeak	Jonathan Cairns	Bayesian Analysis of ChIP-seq Data
baySeq	Thomas J. Hardcastle	Empirical Bayesian analysis of patterns of differential expression in count data
BCRANK	Adam Ameur	Predicting binding site consensus from ranked DNA sequences
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
BEAT	Kemal Akman	BEAT - BS-Seq Epimutation Analysis Toolkit
BEclear	Markus Merl	Correct for batch effects in DNA methylation data
betr	Martin Aryee	Identify differentially expressed genes in microarray time-course data
bgafun	Iain Wallace	BGAfun A method to identify specifity determining residues in protein families
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
BiGGR	Anand K. Gavai, Hannes Hettling	Constraint based modeling in R using metabolic reconstruction databases.
bigmemoryExtras	Peter M. Haverty	An extension of the bigmemory package with added safety, convenience, and a factor class.
bioassayR	Tyler Backman	R library for Bioactivity analysis
Biobase	Bioconductor Package Maintainer	Biobase: Base functions for Bioconductor
BiocCaseStudies	Bioconductor Package Maintainer	BiocCaseStudies: Support for the Case Studies Monograph
BiocCheck	Bioconductor Package Maintainer	Bioconductor-specific package checks
BiocGenerics	Bioconductor Package Maintainer	S4 generic functions for Bioconductor
biocGraph	Florian Hahne	Graph examples and use cases in Bioinformatics
BiocInstaller	Bioconductor Package Maintainer	Install/Update Bioconductor and CRAN Packages
BiocParallel	Bioconductor Package Maintainer	Bioconductor facilities for parallel evaluation
BiocStyle	Bioconductor Package Maintainer	Standard styles for vignettes and other Bioconductor documents
biocViews	Bioconductor Package Maintainer	Categorized views of R package repositories
bioDist	Bioconductor Package Maintainer	Different distance measures
biomaRt	Steffen Durinck	Interface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase and Gramene)
BioMVCClass	Elizabeth Whalen	Model-View-Controller (MVC) Classes That Use Biobase
biomvRCNS	Yang Du	Copy Number study and Segmentation for multivariate biological data
BioNet	Marcus Dittrich	Routines for the functional analysis of biological networks
BioSeqClass	Li Hong	Classification for Biological Sequences
Biostrings	H. Pages	String objects representing biological sequences, and matching algorithms
biosvd	Anneleen Daemen, Matthew Brauer	Package for high-throughput data processing, outlier detection, noise removal and dynamic modeling
biovizBase	Tengfei Yin	Basic graphic utilities for visualization of genomic data.
BiRewire	Andrea Gobbi	High-performing routines for the randomization of a bipartite graph (or a binary event matrix) and directed signed graph preserving degree distribution (or marginal totals).
birta	Benedikt Zacher, Holger Froehlich	Bayesian Inference of Regulation of Transcriptional Activity
birte	Holger Froehlich	Bayesian Inference of Regulatory Influence on Expression (biRte)
BiSeq	Katja Hebestreit	Processing and analyzing bisulfite sequencing data
BitSeq	Antti Honkela, Panagiotis Papastamoulis	Transcript expression inference and differential expression analysis for RNA-seq data
blima	Vojtech Kulvait	Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.
BRAIN	Piotr Dittwald	Baffling Recursive Algorithm for Isotope distributioN calculations
BrainStars	Itoshi NIKAIDO	query gene expression data and plots from BrainStars (B*)
bridge	Raphael Gottardo	Bayesian Robust Inference for Differential Gene Expression
BridgeDbR	Anwesha Bohler	Code for using BridgeDb identifier mapping framework from within R
BrowserViz	Paul Shannon	BrowserViz: interactive R/browser graphics using websockets and JSON
BrowserVizDemo	Paul Shannon	BrowserVizDemo: How to subclass BrowserViz
BSgenome	H. Pages	Infrastructure for Biostrings-based genome data packages
bsseq	Kasper Daniel Hansen	Analyze, manage and store bisulfite sequencing data.
BubbleTree	Wei Zhu	A method to elucidate purity and clonality in tumors using copy number ratio and allele frequency
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
bumphunter	Rafael A. Irizarry	Bump Hunter
BUS	Yuanhua Liu	Gene network reconstruction
CAFE	Sander Bollen	Chromosmal Aberrations Finder in Expression data
CAGEr	Vanja Haberle	Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
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
canceR	Karim Mezhoud	A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC.
cancerclass	Daniel Kosztyla	Development and validation of diagnostic tests from high-dimensional molecular data
CancerMutationAnalysis	Simina M. Boca	Cancer mutation analysis
CAnD	Caitlin McHugh	Perform Chromosomal Ancestry Differences (CAnD) Analyses
Cardinal	Kyle D. Bemis	A mass spectrometry imaging toolbox for statistical analysis
casper	David Rossell	Characterization of Alternative Splicing based on Paired-End Reads
Category	Bioconductor Package Maintainer	Category Analysis
categoryCompare	Robert M. Flight	Meta-analysis of high-throughput experiments using feature annotations
ccrepe	Emma Schwager,Craig Bielski, George Weingart	ccrepe_and_nc.score
cellGrowth	Julien Gagneur	Fitting cell population growth models
cellHTS	Ligia Bras	Analysis of cell-based screens
cellHTS2	Joseph Barry	Analysis of cell-based screens - revised version of cellHTS
CellNOptR	T.Cokelaer	Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.
CexoR	Pedro Madrigal	An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
CFAssay	Herbert Braselmann	Statistical analysis for the Colony Formation Assay
CGEN	William Wheeler	An R package for analysis of case-control studies in genetic epidemiology
CGHbase	Mark van de Wiel	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.
ChAMP	Tiffany Morris	Chip Analysis Methylation Pipeline for Illumina HumanMethylation450
charm	Peter Murakami	Analysis of DNA methylation data from CHARM microarrays
ChemmineOB	Thomas Girke	R interface to a subset of OpenBabel functionalities
ChemmineR	Thomas Girke	Cheminformatics Toolkit for R
chimera	Raffaele A Calogero	A package for secondary analysis of fusion products
chipenrich	Ryan P. Welch, Chee Lee, Raymond G. Cavalcante	Gene set enrichment for ChIP-seq peak data
ChIPpeakAnno	Lihua Julie Zhu, Jianhong Ou	Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges.
ChIPQC	Tom Carroll, Rory Stark	Quality metrics for ChIPseq data
ChIPseeker	Guangchuang Yu	ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
chipseq	Bioconductor Package Maintainer	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
ChIPXpress	George Wu	ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
chopsticks	Hin-Tak Leung	The snp.matrix and X.snp.matrix classes
chroGPS	Oscar Reina	chroGPS: visualizing the epigenome
chromDraw	Jan Janecka	chromDraw an R package for visualization of linear and circular karyotypes.
ChromHeatMap	Tim F. Rayner	Heat map plotting by genome coordinate
cisPath	Likun Wang	Visualization and management of the protein-protein interaction networks.
ClassifyR	Dario Strbenac	A framework for two-class classification problems, with applications to differential variability and differential distribution testing.
cleanUpdTSeq	Sarah Sheppard ; Jianhong Ou ; Lihua Julie Zhu	This package classifies putative polyadenylation sites as true or false/internally oligodT primed.
cleaver	Sebastian Gibb	Cleavage of Polypeptide Sequences
clippda	Stephen Nyangoma	A package for the clinical proteomic profiling data analysis
clipper	Paolo Martini	Gene Set Analysis Exploiting Pathway Topology
Clomial	Habil Zare	Infers clonal composition of a tumor
Clonality	Irina Ostrovnaya	Clonality testing
clonotypeR	Charles Plessy	High throughput analysis of T cell antigen receptor sequences
clst	Noah Hoffman	Classification by local similarity threshold
clstutils	Noah Hoffman	Tools for performing taxonomic assignment.
clusterProfiler	Guangchuang Yu	statistical analysis and visulization of functional profiles for genes and gene clusters
clusterStab	James W. MacDonald	Compute cluster stability scores for microarray data
CMA	Christoph Bernau	Synthesis of microarray-based classification
cn.farms	Andreas Mitterecker	cn.FARMS - factor analysis for copy number estimation
cn.mops	Guenter Klambauer	cn.mops - Mixture of Poissons for CNV detection in NGS data
CNAnorm	Stefano Berri	A normalization method for Copy Number Aberration in cancer samples
CNEr	Ge Tan	CNE detection and visualization.
CNORdt	A. MacNamara	Add-on to CellNOptR: Discretized time treatments
CNORfeeder	F.Eduati	Integration of CellNOptR to add missing links
CNORfuzzy	T. Cokelaer	Addon to CellNOptR: Fuzzy Logic
CNORode	David Henriques	ODE add-on to CellNOptR
CNTools	J. Zhang	Convert segment data into a region by sample matrix to allow for other high level computational analyses.
cnvGSA	Joseph Lugo	Gene Set Analysis of (Rare) Copy Number Variants
CNVrd2	Hoang Tan Nguyen	CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.
CNVtools	Chris Barnes	A package to test genetic association with CNV data
cobindR	Manuela Benary	Finding Co-occuring motifs of transcription factor binding sites
CoCiteStats	Bioconductor Package Maintainer	Different test statistics based on co-citation.
codelink	Diego Diez	Manipulation of Codelink microarray data.
CODEX	Yuchao Jiang	A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
CoGAPS	Elana J. Fertig, Michael F. Ochs	Coordinated Gene Activity in Pattern Sets
cogena	Zhilong Jia	co-expressed gene-set enrichment analysis
coGPS	Yingying Wei	cancer outlier Gene Profile Sets
COHCAP	Charles Warden	CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
coMET	Tiphaine Martin	coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.
COMPASS	Greg Finak	Combinatorial Polyfunctionality Analysis of Single Cells
compcodeR	Charlotte Soneson	RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
compEpiTools	Kamal Kishore	Tools for computational epigenomics
CompGO	Ashley J. Waardenberg	An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
ComplexHeatmap	Zuguang Gu	Making Complex Heatmaps
ConsensusClusterPlus	Matt Wilkerson	ConsensusClusterPlus
conumee	Volker Hovestadt	Enhanced copy-number variation analysis using Illumina 450k methylation arrays
convert	Yee Hwa (Jean) Yang	Convert Microarray Data Objects
copa	James W. MacDonald	Functions to perform cancer outlier profile analysis.
copynumber	Gro Nilsen	Segmentation of single- and multi-track copy number data by penalized least squares regression.
CopyNumber450k	Simon Papillon-Cavanagh	R package for calling CNV from Illumina 450k methylation microarrays
CopywriteR	Thomas Kuilman	Copy number information from targeted sequencing using off-target reads
CoRegNet	Remy Nicolle	CoRegNet : reconstruction and integrated analysis of co-regulatory networks
Cormotif	Yingying Wei	Correlation Motif Fit
CorMut	Zhenpeng Li	Detect the correlated mutations based on selection pressure
coRNAi	Elin Axelsson	Analysis of co-knock-down RNAi data
CORREP	Dongxiao Zhu	Multivariate Correlation Estimator and Statistical Inference Procedures.
cosmiq	David Fischer, Christian Panse	cosmiq - COmbining Single Masses Into Quantities
COSNet	Marco Frasca	Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings
CoverageView	Ernesto Lowy	Coverage visualization package for R
cpvSNP	Caitlin McHugh	Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
cqn	Kasper Daniel Hansen	Conditional quantile normalization
CRImage	Henrik Failmezger, Yinyin Yuan	CRImage a package to classify cells and calculate tumour cellularity
CRISPRseek	Lihua Julie Zhu	Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
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
csaw	Aaron Lun	ChIP-seq analysis with windows
CSSP	Chandler Zuo	ChIP-Seq Statistical Power
ctc	Antoine Lucas	Cluster and Tree Conversion.
cummeRbund	Loyal A. Goff	Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
customProDB	xiaojing wang	Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search.
cycle	Matthias Futschik	Significance of periodic expression pattern in time-series data
cytofkit	Jinmiao Chen	cytofkit: an integrated analysis pipeline for mass cytometry data
dagLogo	Jianhong Ou	dagLogo
daMA	Jobst Landgrebe	Efficient design and analysis of factorial two-colour microarray data
DART	Charles Shijie Zheng	Denoising Algorithm based on Relevance network Topology
DASiR	Oscar Flores, Anna Mantsoki	Distributed Annotation System in R
DAVIDQuery	Roger Day	Retrieval from the DAVID bioinformatics data resource into R
DBChIP	Kun Liang	Differential Binding of Transcription Factor with ChIP-seq
ddCt	Jitao David Zhang	The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
ddgraph	Robert Stojnic	Distinguish direct and indirect interactions with Graphical Modelling
DECIPHER	Erik Wright	Database Enabled Code for Ideal Probe Hybridization Employing R
DeconRNASeq	Ting Gong	Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
DEDS	Yuanyuan Xiao	Differential Expression via Distance Summary for Microarray Data
deepSNV	Moritz Gerstung	Detection of subclonal SNVs in deep sequencing data.
DEGraph	Laurent Jacob	Two-sample tests on a graph
DEGreport	Lorena Pantano	Report of DEG analysis
DEGseq	Likun Wang	Identify Differentially Expressed Genes from RNA-seq data
deltaGseg	Diana Low	deltaGseg
derfinder	Leonardo Collado-Torres	Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution
derfinderHelper	Leonardo Collado-Torres	derfinder helper package
derfinderPlot	Leonardo Collado-Torres	Plotting functions for derfinder
DESeq	Simon Anders	Differential gene expression analysis based on the negative binomial distribution
DESeq2	Michael Love	Differential gene expression analysis based on the negative binomial distribution
DEXSeq	Alejandro Reyes	Inference of differential exon usage in RNA-Seq
dexus	Guenter Klambauer	DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
DFP	Rodrigo Alvarez-Glez	Gene Selection
DiffBind	Rory Stark	Differential Binding Analysis of ChIP-Seq peak data
diffGeneAnalysis	Choudary Jagarlamudi	Performs differential gene expression Analysis
diffHic	Aaron Lun	Differential analyis of Hi-C data
diggit	Mariano J Alvarez	Inference of Genetic Variants Driving Cellular Phenotypes
DirichletMultinomial	Martin Morgan	Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
dks	Jeffrey T. Leek	The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.
DMRcaller	Nicolae Radu Zabet	Differentially Methylated Regions caller
DMRcate	Tim Peters	Illumina 450K methylation array spatial analysis methods
DMRforPairs	Martin Rijlaarsdam	DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
DNAcopy	Venkatraman E. Seshan	DNA copy number data analysis
domainsignatures	Florian Hahne	Geneset enrichment based on InterPro domain signatures
DOQTL	Daniel Gatti	Genotyping and QTL Mapping in DO Mice
DOSE	Guangchuang Yu	Disease Ontology Semantic and Enrichment analysis
DriverNet	Jiarui Ding	Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer
DrugVsDisease	j. Saez-Rodriguez	Comparison of disease and drug profiles using Gene set Enrichment Analysis
DSS	Hao Wu	Dispersion shrinakge for sequencing data.
DTA	Bjoern Schwalb	Dynamic Transcriptome Analysis
dualKS	Eric J. Kort, Yarong Yang	Dual KS Discriminant Analysis and Classification
DupChecker	"Quanhu SHENG"	a package for checking high-throughput genomic data redundancy in meta-analysis
dyebias	Philip Lijnzaad	The GASSCO method for correcting for slide-dependent gene-specific dye bias
DynDoc	Bioconductor Package Maintainer	Dynamic document tools
EasyqpcR	Le Pape Sylvain	EasyqpcR for low-throughput real-time quantitative PCR data analysis
easyRNASeq	Nicolas Delhomme	Count summarization and normalization for RNA-Seq data
EBarrays	Ming Yuan	Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
EBcoexpress	John A. Dawson	EBcoexpress for Differential Co-Expression Analysis
EBImage	Andrzej Oleś	Image processing and analysis toolbox for R
EBSeq	Ning Leng	An R package for gene and isoform differential expression analysis of RNA-seq data
EBSeqHMM	Ning Leng	Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
ecolitk	Laurent Gautier	Meta-data and tools for E. coli
EDASeq	Davide Risso	Exploratory Data Analysis and Normalization for RNA-Seq
EDDA	Chia Kuan Hui Burton, Niranjan Nagarajan	Experimental Design in Differential Abundance analysis
edge	John D. Storey	Extraction of Differential Gene Expression
edgeR	Yunshun Chen, Aaron Lun, Mark Robinson, Davis McCarthy, Gordon Smyth	Empirical analysis of digital gene expression data in R
eiR	Thomas Girke	Accelerated similarity searching of small molecules
eisa	Gabor Csardi	Expression data analysis via the Iterative Signature Algorithm
ELBOW	Graham Alvare, Xiangli Zhang	ELBOW - Evaluating foLd change By the lOgit Way
EMDomics	Daniel Schmolze	Earth Mover's Distance for Differential Analysis of Genomics Data
ENCODExplorer	Charles Joly Beauparlant	A compilation of ENCODE metadata
ENmix	Zongli Xu	Data preprocessing and quality control for Illumina HumanMethylation450 BeadChip
EnrichmentBrowser	Ludwig Geistlinger	Seamless navigation through combined results of set-based and network-based enrichment analysis
ensembldb	Johannes Rainer	Utilities to create and use an Ensembl based annotation database
ensemblVEP	Valerie Obenchain	R Interface to Ensembl Variant Effect Predictor
ENVISIONQuery	Alex Lisovich, Roger Day	Retrieval from the ENVISION bioinformatics data portal into R
epigenomix	Hans-Ulrich Klein	Epigenetic and gene transcription data normalization and integration with mixture models
epivizr	Hector Corrada Bravo	R Interface to epiviz web app
erccdashboard	Sarah Munro	Assess Differential Gene Expression Experiments with ERCC Controls
ExiMiR	Sylvain Gubian	R functions for the normalization of Exiqon miRNA array data
exomeCopy	Michael Love	Copy number variant detection from exome sequencing read depth
exomePeak	Jia Meng	exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis
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
facopy	David Mosen-Ansorena	Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
factDesign	Denise Scholtens	Factorial designed microarray experiment analysis
farms	Djork-Arne Clevert	FARMS - Factor Analysis for Robust Microarray Summarization
fastLiquidAssociation	Tina Gunderson	functions for genome-wide application of Liquid Association
fastseg	Guenter Klambauer	fastseg - a fast segmentation algorithm
fdrame	Effi Kenigsberg	FDR adjustments of Microarray Experiments (FDR-AME)
FEM	Andrew E. Teschendorff	Identification of Functional Epigenetic Modules
ffpe	Levi Waldron	Quality assessment and control for FFPE microarray expression data
FGNet	Sara Aibar	Functional Gene Networks derived from biological enrichment analyses
FISHalyseR	Karesh Arunakirinathan, Andreas Heindl	FISHalyseR a package for automated FISH quantification
flagme	Mark Robinson, Riccardo Romoli	Analysis of Metabolomics GC/MS Data
flipflop	Elsa Bernard	Fast lasso-based isoform prediction as a flow problem
flowBeads	Nikolas Pontikos	flowBeads: Analysis of flow bead data
flowBin	Kieran O'Neill	Combining multitube flow cytometry data by binning
flowcatchR	Federico Marini	Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
flowCHIC	Author: Joachim Schumann	Analyze flow cytometric data using histogram information
flowCL	Justin Meskas	Semantic labelling of flow cytometric cell populations
flowClean	Kipper Fletez-Brant	flowClean
flowClust	Greg Finak, Mike Jiang	Clustering for Flow Cytometry
flowCore	M.Jiang	flowCore: Basic structures for flow cytometry data
flowCyBar	Joachim Schumann	Analyze flow cytometric data using gate information
flowDensity	Mehrnoush Malek	Sequential Flow Cytometry Data Gating
flowFit	Davide Rambaldi	Estimate proliferation in cell-tracking dye studies
flowFP	Herb Holyst	Fingerprinting for Flow Cytometry
flowMap	Chiaowen Joyce Hsiao	Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test
flowMatch	Ariful Azad	Matching and meta-clustering in flow cytometry
flowMeans	Nima Aghaeepour	Non-parametric Flow Cytometry Data Gating
flowMerge	Greg Finak	Cluster Merging for Flow Cytometry Data
flowPeaks	Yongchao Ge	An R package for flow data clustering
flowPlots	N. Hawkins	flowPlots: analysis plots and data class for gated flow cytometry data
flowQ	Mike Jiang	Quality control for flow cytometry
flowQB	Faysal El Khettabi	Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CVinstrinsic calculations.
FlowRepositoryR	Josef Spidlen	FlowRepository R Interface
FlowSOM	Sofie Van Gassen	Using self-organizing maps for visualization and interpretation of cytometry data
flowStats	Greg Finak and Mike Jiang	Statistical methods for the analysis of flow cytometry data
flowTrans	Greg Finak	Parameter Optimization for Flow Cytometry Data Transformation
flowType	Nima Aghaeepour	Phenotyping Flow Cytometry Assays
flowUtils	Josef Spidlen	Utilities for flow cytometry
flowViz	Mike Jiang	Visualization for flow cytometry
flowVS	Ariful Azad	Variance stabilization in flow cytometry (and microarrays)
flowWorkspace	Greg Finak,Mike Jiang	Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore
fmcsR	Thomas Girke	Mismatch Tolerant Maximum Common Substructure Searching
focalCall	Oscar Krijgsman	Detection of focal aberrations in DNA copy number data
FourCSeq	Felix A. Klein	Package analyse 4C sequencing data
FRGEpistasis	Futao Zhang	Epistasis Analysis for Quantitative Traits by Functional Regression Model
frma	Matthew N. McCall	Frozen RMA and Barcode
frmaTools	Matthew N. McCall	Frozen RMA Tools
FunciSNP	Simon G. Coetzee	Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs
gaga	David Rossell	GaGa hierarchical model for high-throughput data analysis
gage	Weijun Luo	Generally Applicable Gene-set Enrichment for Pathway Analysis
gaggle	Christopher Bare	Broadcast data between R and Gaggle
gaia	S. Morganella	GAIA: An R package for genomic analysis of significant chromosomal aberrations.
gaucho	Alex Murison, Christopher Wardell	Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering
gCMAP	Thomas Sandmann	Tools for Connectivity Map-like analyses
gCMAPWeb	Thomas Sandmann	A web interface for gene-set enrichment analyses
gcrma	Z. Wu	Background Adjustment Using Sequence Information
gdsfmt	Xiuwen Zheng	R Interface to CoreArray Genomic Data Structure (GDS) Files
geecc	Markus Boenn	Gene set Enrichment analysis Extended to Contingency Cubes
genArise	IFC Development Team	Microarray Analysis tool
GENE.E	Joshua Gould	Interact with GENE-E from R
GeneAnswers	Lei Huang and Gang Feng	Integrated Interpretation of Genes
GeneExpressionSignature	Yang Cao, Fei Li,Lu Han	Gene Expression Signature based Similarity Metric
genefilter	Bioconductor Package Maintainer	genefilter: methods for filtering genes from high-throughput experiments
genefu	Benjamin Haibe-Kains, Markus Schroeder	Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer.
GeneGA	Zhenpeng Li	Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
GeneMeta	Bioconductor Package Maintainer	MetaAnalysis for High Throughput Experiments
GeneNetworkBuilder	Jianhong Ou	Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
GeneOverlap	Li Shen, Mount Sinai	Test and visualize gene overlaps
geneplotter	Bioconductor Package Maintainer	Graphics related functions for Bioconductor
geneRecommender	Greg Hather	A gene recommender algorithm to identify genes coexpressed with a query set of genes
GeneRegionScan	Lasse Folkersen	GeneRegionScan
geneRxCluster	Charles Berry	gRx Differential Clustering
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
GENESIS	Matthew P. Conomos	GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
geNetClassifier	Sara Aibar	classify diseases and build associated gene networks using gene expression profiles
GeneticsDesign	The R Genetics Project	Functions for designing genetics studies
GeneticsPed	David Henderson	Pedigree and genetic relationship functions
genoCN	Wei Sun	genotyping and copy number study tools
genomation	Altuna Akalin, Vedran Franke	Summary, annotation and visualization of genomic data
GenomeGraphs	Steffen Durinck	Plotting genomic information from Ensembl
GenomeInfoDb	Bioconductor Package Maintainer	Utilities for manipulating chromosome and other 'seqname' identifiers
genomeIntervals	Julien Gagneur	Operations on genomic intervals
genomes	Chris Stubben	Genome sequencing project metadata
GenomicAlignments	Bioconductor Package Maintainer	Representation and manipulation of short genomic alignments
GenomicFeatures	Bioconductor Package Maintainer	Tools for making and manipulating transcript centric annotations
GenomicFiles	Bioconductor Package Maintainer	Distributed computing by file or by range
GenomicInteractions	Malcolm Perry, Liz Ing-Simmons	R package for handling genomic interaction data
GenomicRanges	Bioconductor Package Maintainer	Representation and manipulation of genomic intervals
GenomicTuples	Peter Hickey	Representation and Manipulation of Genomic Tuples
Genominator	James Bullard	Analyze, manage and store genomic data
genoset	Peter M. Haverty	Provides classes similar to ExpressionSet for copy number analysis
GenoView	Sharon Lee	Condensed, overlapped plotting of genomic data tracks
GEOmetadb	Jack Zhu	A compilation of metadata from NCBI GEO
GEOquery	Sean Davis	Get data from NCBI Gene Expression Omnibus (GEO)
GEOsubmission	Alexandre Kuhn	Prepares microarray data for submission to GEO
gespeR	Fabian Schmich	Gene-Specific Phenotype EstimatoR
GEWIST	Wei Q. Deng	Gene Environment Wide Interaction Search Threshold
GGBase	VJ Carey	GGBase infrastructure for genetics of gene expression package GGtools
ggbio	Tengfei Yin	Visualization tools for genomic data.
GGtools	VJ Carey	software and data for analyses in genetics of gene expression
ggtree	Guangchuang Yu	a phylogenetic tree viewer for different types of tree annotations
girafe	J. Toedling	Genome Intervals and Read Alignments for Functional Exploration
GLAD	Philippe Hupe	Gain and Loss Analysis of DNA
GlobalAncova	Manuela Hummel	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
gmapR	Michael Lawrence	An R interface to the GMAP/GSNAP/GSTRUCT suite
GOexpress	Kevin Rue-Albrecht	Visualise microarray and RNAseq data using gene ontology annotations
GOFunction	Jing Wang	GO-function: deriving biologcially relevant functions from statistically significant functions
GoogleGenomics	Siddhartha Bagaria	R Client for Google Genomics API
goProfiles	Alex Sanchez	goProfiles: an R package for the statistical analysis of functional profiles
GOSemSim	Guangchuang Yu	GO-terms Semantic Similarity Measures
goseq	Nadia Davidson	Gene Ontology analyser for RNA-seq and other length biased data
GOSim	Holger Froehlich	Computation of functional similarities between GO terms and gene products; GO enrichment analysis
GOstats	Bioconductor Package Maintainer	Tools for manipulating GO and microarrays.
GOsummaries	Raivo Kolde	Word cloud summaries of GO enrichment analysis
GOTHiC	Borbala Mifsud	Binomial test for Hi-C data analysis
goTools	Agnes Paquet	Functions for Gene Ontology database
gpls	Bioconductor Package Maintainer	Classification using generalized partial least squares
gprege	Alfredo Kalaitzis	Gaussian Process Ranking and Estimation of Gene Expression time-series
gQTLBase	VJ Carey	gQTLBase: infrastructure for eQTL, mQTL and similar studies
gQTLstats	VJ Carey	gQTLstats: computationally efficient analysis for eQTL and allied studies
graph	Bioconductor Package Maintainer	graph: A package to handle graph data structures
GraphAlignment	Joern P. Meier	GraphAlignment
GraphAT	Thomas LaFramboise	Graph Theoretic Association Tests
graphite	Gabriele Sales	GRAPH Interaction from pathway Topological Environment
GraphPAC	Gregory Ryslik	Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.
GRENITS	Edward Morrissey	Gene Regulatory Network Inference Using Time Series
GreyListChIP	Gordon Brown	Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
groHMM	Anusha Nagari, W. Lee Kraus	GRO-seq Analysis Pipeline.
GSAR	Yasir Rahmatallah, Galina Glazko	Gene Set Analysis in R
GSCA	Zhicheng Ji	GSCA: Gene Set Context Analysis
GSEABase	Bioconductor Package Maintainer	Gene set enrichment data structures and methods
GSEAlm	Assaf Oron	Linear Model Toolset for Gene Set Enrichment Analysis
GSReg	Bahman Afsari	Gene Set Regulation (GS-Reg)
GSRI	Julian Gehring	Gene Set Regulation Index
GSVA	Justin Guinney	Gene Set Variation Analysis for microarray and RNA-seq data
gtrellis	Zuguang Gu	Genome Level Trellis Layout
Gviz	Florian Hahne	Plotting data and annotation information along genomic coordinates
gwascat	VJ Carey	representing and modeling data in the NHGRI GWAS catalog
GWASTools	Stephanie M. Gogarten, Adrienne Stilp	Tools for Genome Wide Association Studies
h5vc	Paul Theodor Pyl	Managing alignment tallies using a hdf5 backend
hapFabia	Sepp Hochreiter	hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
Harshlight	Maurizio Pellegrino	A "corrective make-up" program for microarray chips
HCsnip	Askar Obulkasim	Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree
HDTD	Anestis Touloumis	Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Heatplus	Alexander Ploner	Heatmaps with row and/or column covariates and colored 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
hiAnnotator	Nirav V Malani	Functions for annotating GRanges objects.
HIBAG	Xiuwen Zheng	HLA Genotype Imputation with Attribute Bagging
HilbertVis	Simon Anders	Hilbert curve visualization
HilbertVisGUI	Simon Anders	HilbertVisGUI
hiReadsProcessor	Nirav V Malani	Functions to process LM-PCR reads from 454/Illumina data.
HiTC	Nicolas Servant	High Throughput Chromosome Conformation Capture analysis
HMMcopy	Daniel Lai, Gavin Ha, Sohrab Shah	Copy number prediction with correction for GC and mappability bias for HTS data
hopach	Katherine S. Pollard	Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
hpar	Laurent Gatto	Human Protein Atlas in R
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
HTSeqGenie	Jens Reeder	A NGS analysis pipeline.
htSeqTools	Oscar Reina	Quality Control, Visualization and Processing for High-Throughput Sequencing data
HTSFilter	Andrea Rau	Filter replicated high-throughput transcriptome sequencing data
HybridMTest	Demba Fofana	Hybrid Multiple Testing
hyperdraw	Paul Murrell	Visualizing Hypergaphs
hypergraph	Bioconductor Package Maintainer	A package providing hypergraph data structures
iASeq	Yingying Wei	iASeq: integrating multiple sequencing datasets for detecting allele-specific events
iBBiG	Aedin Culhane	Iterative Binary Biclustering of Genesets
ibh	Kircicegi Korkmaz	Interaction Based Homogeneity for Evaluating Gene Lists
iBMQ	Greg Imholte	integrated Bayesian Modeling of eQTL data
Icens	Bioconductor Package Maintainer	NPMLE for Censored and Truncated Data
iChip	Qianxing Mo	Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
iClusterPlus	Qianxing Mo, Ronglai Shen	Integrative clustering of multi-type genomic data
IdeoViz	Shraddha Pai	Plots data (continuous/discrete) along chromosomal ideogram
idiogram	Karl J. Dykema	idiogram
IdMappingAnalysis	Alex Lisovich, Roger Day	ID Mapping Analysis
IdMappingRetrieval	Alex Lisovich, Roger Day	ID Mapping Data Retrieval
illuminaio	Kasper Daniel Hansen	Parsing Illumina microarray output files
imageHTS	Joseph Barry	Analysis of high-throughput microscopy-based screens
immunoClust	Till Soerensen	immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
IMPCdata	Jeremy Mason	Retrieves data from IMPC database
impute	Balasubramanian Narasimhan	impute: Imputation for microarray data
InPAS	Jianhong Ou	Identification of Novel alternative PolyAdenylation Sites (PAS)
INPower	Bill Wheeler	An R package for computing the number of susceptibility SNPs
inSilicoDb	InSilico DB	Access to the InSilico Database
inSilicoMerging	InSilico DB	Collection of Merging Techniques for Gene Expression Data
intansv	Wen Yao	Integrative analysis of structural variations
interactiveDisplay	Shawn Balcome	Package for enabling powerful shiny web displays of Bioconductor objects
interactiveDisplayBase	Shawn Balcome	Base package for enabling powerful shiny web displays of Bioconductor objects
inveRsion	Alejandro Caceres	Inversions in genotype data
iontree	Mingshu Cao	Data management and analysis of ion trees from ion-trap mass spectrometry
iPAC	Gregory Ryslik	Identification of Protein Amino acid Clustering
IPPD	Martin Slawski	Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching
IRanges	Bioconductor Package Maintainer	Infrastructure for manipulating intervals on sequences
iSeq	Qianxing Mo	Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
isobar	Florian P Breitwieser	Analysis and quantitation of isobarically tagged MSMS proteomics 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
IVAS	Seonggyun Han	Identification of genetic Variants affecting Alternative Splicing
jmosaics	Xin Zeng	Joint analysis of multiple ChIP-Seq data sets
joda	Ewa Szczurek	JODA algorithm for quantifying gene deregulation using knowledge
KCsmart	Jorma de Ronde	Multi sample aCGH analysis package using kernel convolution
kebabs	Ulrich Bodenhofer	Kernel-Based Analysis Of Biological Sequences
KEGGgraph	Jitao David Zhang	KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
keggorthology	VJ Carey	graph support for KO, KEGG Orthology
KEGGprofile	Shilin Zhao	An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway
KEGGREST	Bioconductor Package Maintainer	Client-side REST access to KEGG
lapmix	Yann Ruffieux	Laplace Mixture Model in Microarray Experiments
LBE	Cyril Dalmasso	Estimation of the false discovery rate.
LEA	Eric Frichot	LEA: an R package for Landscape and Ecological Association Studies
les	Julian Gehring	Identifying Differential Effects in Tiling Microarray Data
limma	Gordon Smyth	Linear Models for Microarray Data
limmaGUI	Keith Satterley	GUI for limma package
LiquidAssociation	Yen-Yi Ho	LiquidAssociation
lmdme	Cristobal Fresno	Linear Model decomposition for Designed Multivariate Experiments
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
lol	Yinyin Yuan	Lots Of Lasso
LowMACA	Stefano de Pretis, Giorgio Melloni	LowMACA - Low frequency Mutation Analysis via Consensus Alignment
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.
lpNet	Bettina Knapp	Linear Programming Model for Network Inference
lumi	Pan Du	BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
LVSmiRNA	Stefano Calza	LVS normalization for Agilent miRNA data
M3D	Tom Mayo	Identifies differentially methylated regions across testing groups.
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
made4	Aedin Culhane	Multivariate analysis of microarray data using ADE4
maigesPack	Gustavo H. Esteves	Functions to handle cDNA microarray data, including several methods of data analysis
MAIT	Francesc Fernandez-Albert	Statistical Analysis of Metabolomic Data
makecdfenv	James W. MacDonald	CDF Environment Maker
MANOR	Pierre Neuvial	CGH Micro-Array NORmalization
manta	Chris Berthiaume, Adrian Marchetti	Microbial Assemblage Normalized Transcript Analysis
MantelCorr	Brian Steinmeyer	Compute Mantel Cluster Correlations
mAPKL	Argiris Sakellariou	A Hybrid Feature Selection method for gene expression data
maPredictDSC	Adi Laurentiu Tarca	Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge
marray	Yee Hwa (Jean) Yang	Exploratory analysis for two-color spotted microarray data
maSigPro	Maria Jose Nueda	Significant Gene Expression Profile Differences in Time Course Microarray Data
maskBAD	Michael Dannemann	Masking probes with binding affinity differences
MassArray	Reid F. Thompson	Analytical Tools for MassArray Data
massiR	Sam Buckberry	massiR: MicroArray Sample Sex Identifier
MassSpecWavelet	Pan Du	Mass spectrum processing by wavelet-based algorithms
matchBox	Luigi Marchionni, Anuj Gupta	Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.
MatrixRider	Elena Grassi	Obtain total affinity and occupancies for binding site matrices on a given sequence
MBAmethyl	Tao Wang	Model-based analysis of DNA methylation data
MBASED	Oleg Mayba	Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
MBCB	Jeff Allen	MBCB (Model-based Background Correction for Beadarray)
mBPCR	P.M.V. Rancoita	Bayesian Piecewise Constant Regression for DNA copy number estimation
mcaGUI	Wade K. Copeland	Microbial Community Analysis GUI
MCRestimate	Marc Johannes	Misclassification error estimation with cross-validation
mdgsa	David Montaner	Multi Dimensional Gene Set Analysis.
mdqc	Gabriela Cohen-Freue	Mahalanobis Distance Quality Control for microarrays
MeasurementError.cor	Beiying Ding	Measurement Error model estimate for correlation coefficient
MEDIPS	Lukas Chavez	DNA IP-seq data analysis
MEDME	Mattia Pelizzola	Modelling Experimental Data from MeDIP Enrichment
MEIGOR	Jose Egea	MEIGO - MEtaheuristics for bIoinformatics Global Optimization
MergeMaid	Xiaogang Zhong	Merge Maid
MeSHDbi	Koki Tsuyuzaki	DBI to construct MeSH-related package from sqlite file
meshr	Koki Tsuyuzaki	Tools for conducting enrichment analysis of MeSH
MeSHSim	Jing ZHou	MeSH(Medical Subject Headings) Semantic Similarity Measures
messina	Mark Pinese	Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems.
metaArray	Hyungwon Choi	Integration of Microarray Data for Meta-analysis
Metab	Raphael Aggio	Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
metabomxtr	Michael Nodzenski	A package to run mixture models for truncated metabolomics data with normal or lognormal distributions.
metagene	Charles Joly Beauparlant	A package to produce metagene plots
metagenomeSeq	Joseph N. Paulson	Statistical analysis for sparse high-throughput sequencing
metahdep	John R. Stevens	Hierarchical Dependence in Meta-Analysis
metaMS	Ron Wehrens	MS-based metabolomics annotation pipeline
metaSeq	Koki Tsuyuzaki	Meta-analysis of RNA-Seq count data in multiple studies
metaseqR	Panagiotis Moulos	An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
MethTargetedNGS	Muhammad Ahmer Jamil	Perform Methylation Analysis on Next Generation Sequencing Data
methVisual	Arie Zackay	Methods for visualization and statistics on DNA methylation data
methyAnalysis	Pan Du	DNA methylation data analysis and visualization
MethylAid	M. van Iterson	Visual and interactive quality control of large Illumina 450k data sets
MethylMix	Olivier Gevaert	MethylMix: Identifying methylation driven cancer genes.
methylMnM	Yan Zhou	detect different methylation level (DMR)
methylPipe	Kamal Kishore	Base resolution DNA methylation data analysis
MethylSeekR	Lukas Burger	Segmentation of Bis-seq data
methylumi	Sean Davis	Handle Illumina methylation data
Mfuzz	Matthias Futschik	Soft clustering of time series gene expression data
MGFM	Khadija El Amrani	Marker Gene Finder in Microarray gene expression data
mgsa	Sebastian Bauer	Model-based gene set analysis
MiChip	Jonathon Blake	MiChip Parsing and Summarizing Functions
microRNA	"James F. Reid"	Data and functions for dealing with microRNAs
MIMOSA	Greg Finak	Mixture Models for Single-Cell Assays
MineICA	Anne Biton	Analysis of an ICA decomposition obtained on genomics data
minet	Patrick E. Meyer	Mutual Information NETworks
minfi	Kasper Daniel Hansen	Analyze Illumina's 450k methylation arrays
MinimumDistance	Robert B Scharpf	A package for de novo CNV detection in case-parent trios
MiPP	Sukwoo Kim	Misclassification Penalized Posterior Classification
MiRaGE	Y-h. Taguchi	MiRNA Ranking by Gene Expression
miRNApath	James M. Ward	miRNApath: Pathway Enrichment for miRNA Expression Data
miRNAtap	Maciej Pajak	miRNAtap: microRNA Targets - Aggregated Predictions
Mirsynergy	Yue Li	Mirsynergy
missMethyl	Belinda Phipson, Jovana Maksimovic	Analysis of methylation array data
mitoODE	Gregoire Pau	Implementation of the differential equation model described in "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay"
MLInterfaces	V. Carey	Uniform interfaces to R machine learning procedures for data in Bioconductor containers
MLP	Tobias Verbeke	MLP
MLSeq	Gokmen Zararsiz	Machine learning interface for RNA-Seq data
MMDiff	Gabriele Schweikert	Statistical Testing for ChIP-Seq data sets
mmnet	Yang Cao, Fei Li	A metagenomic pipeline for systems biology
MmPalateMiRNA	Guy Brock	Murine Palate miRNA Expression Analysis
mogsa	Chen Meng	Multiple omics data integration and gene set analysis
monocle	Cole Trapnell	Analysis tools for single-cell expression experiments.
MoPS	Philipp Eser	MoPS - Model-based Periodicity Screening
mosaics	Dongjun Chung	MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
MotifDb	Paul Shannon	An Annotated Collection of Protein-DNA Binding Sequence Motifs
motifRG	Zizhen Yao	A package for discriminative motif discovery, designed for high throughput sequencing dataset
motifStack	Jianhong Ou	Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
MotIV	Eloi Mercier, Raphael Gottardo	Motif Identification and Validation
MPFE	Conrad Burden	Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data.
mQTL.NMR	Lyamine Hedjazi	Metabolomic Quantitative Trait Locus Mapping for 1H NMR data
msa	Ulrich Bodenhofer	Multiple Sequence Alignment
MSGFgui	Thomas Lin Pedersen	A shiny GUI for MSGFplus
MSGFplus	Thomas Lin Pedersen	An interface between R and MS-GF+
msmsEDA	Josep Gregori	Exploratory Data Analysis of LC-MS/MS data by spectral counts
msmsTests	Josep Gregori i Font	LC-MS/MS Differential Expression Tests
MSnbase	Laurent Gatto	Base Functions and Classes for MS-based Proteomics
MSnID	Vlad Petyuk	Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications.
MSstats	Meena Choi	Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Mulcom	Claudio Isella	Calculates Mulcom test
MultiMed	Simina M. Boca	Testing multiple biological mediators simultaneously
multiscan	Mizanur Khondoker	R package for combining multiple scans
multtest	Katherine S. Pollard	Resampling-based multiple hypothesis testing
muscle	Alex T. Kalinka	Multiple Sequence Alignment with MUSCLE
MVCClass	Elizabeth Whalen	Model-View-Controller (MVC) Classes
mvGST	John R. Stevens	Multivariate and directional gene set testing
mygene	Adam Mark, Chunlei Wu	Access MyGene.Info_ services
mzID	Thomas Lin Pedersen	An mzIdentML parser for R
mzR	Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou	parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
NanoStringQCPro	Robert Ziman	Quality metrics and data processing methods for NanoString mRNA gene expression data
NarrowPeaks	Pedro Madrigal	Shape-based Analysis of Variation in ChIP-Seq using Functional PCA
ncdfFlow	Mike Jiang	ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
NCIgraph	Laurent Jacob	Pathways from the NCI Pathways Database
neaGUI	Setia Pramana	An R package to perform the network enrichment analysis (NEA).
nem	Holger Froehlich	(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies
netbenchmark	Pau Bellot	Benchmarking of several gene network inference methods
netbiov	Shailesh tripathi	A package for visualizing complex biological network
nethet	Nicolas Staedler, Frank Dondelinger	A bioconductor package for high-dimensional exploration of biological network heterogeneity
NetPathMiner	Ahmed Mohamed	NetPathMiner for Biological Network Construction, Path Mining and Visualization
netresponse	Leo Lahti	Functional Network Analysis
NetSAM	Bing Zhang	Network Seriation And Modularization
networkBMA	Ka Yee Yeung	Regression-based network inference using Bayesian Model Averaging
NGScopy	Xiaobei Zhao	NGScopy: Detection of Copy Number Variations in Next Generation Sequencing sequencing
nnNorm	Adi Laurentiu Tarca	Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
NOISeq	Sonia Tarazona	Exploratory analysis and differential expression for RNA-seq data
nondetects	Matthew N. McCall	Non-detects in qPCR data
NormqPCR	James Perkins	Functions for normalisation of RT-qPCR data
npGSEA	Jessica Larson	Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
NTW	Yuanhua Liu	Predict gene network using an Ordinary Differential Equation (ODE) based method
nucleR	Ricard Illa	Nucleosome positioning package for R
nudge	N. Dean	Normal Uniform Differential Gene Expression detection
NuPoP	Ji-Ping Wang	An R package for nucleosome positioning prediction
occugene	Oliver Will	Functions for Multinomial Occupancy Distribution
OCplus	Alexander Ploner	Operating characteristics plus sample size and local fdr for microarray experiments
oligo	Benilton Carvalho	Preprocessing tools for oligonucleotide arrays
oligoClasses	Benilton Carvalho and Robert Scharpf	Classes for high-throughput arrays supported by oligo and crlmm
OLIN	Matthias Futschik	Optimized local intensity-dependent normalisation of two-color microarrays
OLINgui	Matthias Futschik	Graphical user interface for OLIN
omicade4	Chen Meng	Multiple co-inertia analysis of omics datasets
OmicCircos	Ying Hu	High-quality circular visualization of omics data
OmicsMarkeR	Charles E. Determan Jr.	Classification and Feature Selection for 'Omics' Datasets
OncoSimulR	Ramon Diaz-Uriarte	Simulation of cancer progresion with order restrictions
oneChannelGUI	Raffaele A Calogero	A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
ontoCAT	Natalja Kurbatova	Ontology traversal and search
openCyto	Mike Jiang	Hierarchical Gating Pipeline for flow cytometry data
oposSOM	Henry Wirth	Comprehensive analysis of transciptome data
OrderedList	Claudio Lottaz	Similarities of Ordered Gene Lists
OrganismDbi	Biocore Data Team	Software to enable the smooth interfacing of different database packages
OSAT	Li Yan	OSAT: Optimal Sample Assignment Tool
OTUbase	Daniel Beck	Provides structure and functions for the analysis of OTU data
OutlierD	Sukwoo Kim	Outlier detection using quantile regression on the M-A scatterplots of high-throughput data
PAA	Michael Turewicz, Martin Eisenacher	PAA (Protein Array Analyzer)
PADOG	Adi Laurentiu Tarca	Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
paircompviz	Michal Burda	Multiple comparison test visualization
pandaR	Dan Schlauch	PANDA algorithm
PAnnBuilder	Li Hong	Protein annotation data package builder
panp	Peter Warren	Presence-Absence Calls from Negative Strand Matching Probesets
PANR	Xin Wang	Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
PAPi	Raphael Aggio	Predict metabolic pathway activity based on metabolomics data
parglms	VJ Carey	support for parallelized estimation of GLMs/GEEs
parody	VJ Carey	Parametric And Resistant Outlier DYtection
pathifier	Assif Yitzhaky	Quantify deregulation of pathways in cancer
PathNet	Jason B. Smith	An R package for pathway analysis using topological information
pathRender	Vince Carey	Render molecular pathways
pathview	Weijun Luo	a tool set for pathway based data integration and visualization
paxtoolsr	Augustin Luna	PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
Pbase	Sebastian Gibb, Laurent Gatto	Manipulating and exploring protein and proteomics data
pcaGoPromoter	Morten Hansen	pcaGoPromoter is used to analyze DNA micro array data
pcaMethods	Henning Redestig	A collection of PCA methods
pcot2	Sarah Song	Principal Coordinates and Hotelling's T-Square method
PCpheno	Nolwenn Le Meur	Phenotypes and cellular organizational units
pdInfoBuilder	Benilton Carvalho	Platform Design Information Package Builder
pdmclass	James W. MacDonald	Classification of Microarray Samples using Penalized Discriminant Methods
PECA	Tomi Suomi	Probe-level Expression Change Averaging
pepStat	Gregory C Imholte	Statistical analysis of peptide microarrays
pepXMLTab	Xiaojing Wang	Parsing pepXML files and filter based on peptide FDR.
PGSEA	Karl Dykema	Parametric Gene Set Enrichment Analysis
phenoDist	Xian Zhang	Phenotypic distance measures
phenoTest	Evarist Planet	Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.
PhenStat	Natasha Karp	Statistical analysis of phenotypic data
phyloseq	Paul J. McMurdie	Handling and analysis of high-throughput microbiome census data.
piano	Leif Varemo	Platform for integrative analysis of omics data
pickgene	Brian S. Yandell	Adaptive Gene Picking for Microarray Expression Data Analysis
PICS	Renan Sauteraud	Probabilistic inference of ChIP-seq
PING	Renan Sauteraud	Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
pint	Olli-Pekka Huovilainen	Pairwise INTegration of functional genomics data
pkgDepTools	Seth Falcon	Package Dependency Tools
plateCore	Errol Strain	Statistical tools and data structures for plate-based flow cytometry
plethy	Daniel Bottomly	R framework for exploration and analysis of respirometry data
plgem	Norman Pavelka	Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
plier	Crispin Miller	Implements the Affymetrix PLIER algorithm
PLPE	Soo-heang Eo	Local Pooled Error Test for Differential Expression with Paired High-throughput Data
plrs	Gwenael G.R. Leday to	Piecewise Linear Regression Splines (PLRS) for the association between DNA copy number and gene expression
plw	Magnus Astrand	Probe level Locally moderated Weighted t-tests.
pmm	Anna Drewek	Parallel Mixed Model
podkat	Ulrich Bodenhofer	Position-Dependent Kernel Association Test
polyester	Alyssa Frazee, Jeff Leek	Simulate RNA-seq reads
Polyfit	Conrad Burden	Add-on to DESeq to improve p-values and q-values
ppiStats	Bioconductor Package Maintainer	Protein-Protein Interaction Statistical Package
prada	Florian Hahne	Data analysis for cell-based functional assays
prebs	Karolis Uziela	Probe region expression estimation for RNA-seq data for improved microarray comparability
PREDA	Francesco Ferrari	Position RElated Data Anlysis
predictionet	Benjamin Haibe-Kains, Catharina Olsen	Inference for predictive networks designed for (but not limited to) genomic data
preprocessCore	Benjamin Milo Bolstad	A collection of pre-processing functions
proBAMr	Xiaojing Wang	Generating SAM file for PSMs in shotgun proteomics data
PROcess	Xiaochun Li	Ciphergen SELDI-TOF Processing
procoil	Ulrich Bodenhofer	Prediction of Oligomerization of Coiled Coil Proteins
ProCoNA	David L Gibbs	Protein co-expression network analysis (ProCoNA).
pRoloc	Laurent Gatto	A unifying bioinformatics framework for spatial proteomics
pRolocGUI	Laurent Gatto, Thomas Naake	Interactive visualisation of spatial proteomics data
PROMISE	Stan Pounds, Xueyuan Cao	PRojection Onto the Most Interesting Statistical Evidence
PROPER	Hao Wu	PROspective Power Evaluation for RNAseq
prot2D	Sebastien Artigaud	Statistical Tools for volume data from 2D Gel Electrophoresis
proteinProfiles	Julian Gehring	Protein Profiling
proteoQC	Bo Wen	An R package for proteomics data quality control
ProtGenerics	Laurent Gatto	S4 generic functions for Bioconductor proteomics infrastructure
PSEA	Alexandre Kuhn	Population-Specific Expression Analysis.
PSICQUIC	Paul Shannon	Protemics Standard Initiative Common QUery InterfaCe
puma	Xuejun Liu	Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
pvac	Jun Lu, Pierre R. Bushel	PCA-based gene filtering for Affymetrix arrays
pvca	Jianying LI	Principal Variance Component Analysis (PVCA)
Pviz	Renan Sauteraud	Peptide Annotation and Data Visualization using Gviz
PWMEnrich	Robert Stojnic	PWM enrichment analysis
pwOmics	Astrid Wachter	Pathway-based data integration of omics data
qcmetrics	Laurent Gatto	A Framework for Quality Control
QDNAseq	Daoud Sie	Quantitative DNA sequencing for chromosomal aberrations
qpcrNorm	Jessica Mar	Data-driven normalization strategies for high-throughput qPCR data.
qpgraph	Robert Castelo	Estimation of genetic and molecular regulatory networks from high-throughput genomics data
qrqc	Vince Buffalo	Quick Read Quality Control
QUALIFIER	Mike Jiang	Quality Control of Gated Flow Cytometry Experiments
quantro	Stephanie Hicks	A test for when to use quantile normalization
quantsmooth	Jan Oosting	Quantile smoothing and genomic visualization of array data
QuartPAC	Gregory Ryslik	Identification of mutational clusters in protein quaternary structures.
QuasR	Michael Stadler	Quantify and Annotate Short Reads in R
qusage	Christopher Bolen	qusage: Quantitative Set Analysis for Gene Expression
qvalue	John D. Storey	Q-value estimation for false discovery rate control
R3CPET	Mohamed Nadhir Djekidel	3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
r3Cseq	Supat Thongjuea	Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
R453Plus1Toolbox	Hans-Ulrich Klein	A package for importing and analyzing data from Roche's Genome Sequencer System
rain	Paul F. Thaben	Rhythmicity Analysis Incorporating Non-parametric Methods
rama	Raphael Gottardo	Robust Analysis of MicroArrays
RamiGO	Markus Schroeder	AmiGO visualize R interface
randPack	Robert Gentleman	Randomization routines for Clinical Trials
RankProd	Fangxin Hong	Rank Product method for identifying differentially expressed genes with application in meta-analysis
Rariant	Julian Gehring	Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
RbcBook1	Vince Carey	Support for Springer monograph on Bioconductor
RBGL	Bioconductor Package Maintainer	An interface to the BOOST graph library
RBioinf	Robert Gentleman	RBioinf
rBiopaxParser	Frank Kramer	Parses BioPax files and represents them in R
RBM	Dongmei Li	RBM: a R package for microarray and RNA-Seq data analysis
Rbowtie	Michael Stadler	R bowtie wrapper
rbsurv	Soo-heang Eo	Robust likelihood-based survival modeling with microarray data
Rcade	Jonathan Cairns	R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data.
RCASPAR	Douaa Mugahid, Lars Kaderali	A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
rcellminer	Augustin Luna, Vinodh Rajapakse	rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
Rchemcpp	Guenter Klambauer	Similarity measures for chemical compounds
RchyOptimyx	Adrin Jalali, Nima Aghaeepour	Optimyzed Cellular Hierarchies for Flow Cytometry
Rcpi	Nan Xiao	Toolkit for Compound-Protein Interaction in Drug Discovery
RCyjs	Paul Shannon	Display and manipulate graphs in Cytoscape.js
RCytoscape	Paul Shannon	Display and manipulate graphs in Cytoscape
RDAVIDWebService	Cristobal Fresno	An R Package for retrieving data from DAVID into R objects using Web Services API.
Rdisop	Steffen Neumann	Decomposition of Isotopic Patterns
RDRToolbox	Christoph Bartenhagen	A package for nonlinear dimension reduction with Isomap and LLE.
ReactomePA	Guangchuang Yu	Reactome Pathway Analysis
ReadqPCR	James Perkins	Read qPCR data
reb	Karl J. Dykema	Regional Expression Biases
RedeR	Mauro Castro	Interactive visualization and manipulation of nested networks
REDseq	Lihua Julie Zhu	Analysis of high-throughput sequencing data processed by restriction enzyme digestion
RefNet	Paul Shannon	A queryable collection of molecular interactions, from many sources
RefPlus	Kai-Ming Chang	A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
regioneR	Bernat Gel	Association analysis of genomic regions based on permutation tests
regionReport	Leonardo Collado-Torres	Generate HTML reports for exploring a set of regions
Repitools	Mark Robinson	Epigenomic tools
ReportingTools	Jason A. Hackney, Gabriel Becker, Jessica L. Larson	Tools for making reports in various formats
ReQON	Christopher Cabanski	Recalibrating Quality Of Nucleotides
rfPred	Hugo Varet	Assign rfPred functional prediction scores to a missense variants list
rGADEM	Arnaud Droit	de novo motif discovery
RGalaxy	Bioconductor Package Maintainer	Make an R function available in the Galaxy web platform
Rgraphviz	Kasper Daniel Hansen	Provides plotting capabilities for R graph objects
rGREAT	Zuguang Gu	Client for GREAT Analysis
RGSEA	Chengcheng Ma	Random Gene Set Enrichment Analysis
rgsepd	Karl Stamm	Gene Set Enrichment / Projection Displays
rhdf5	Bernd Fischer	HDF5 interface to R
Rhtslib	Nathaniel Hayden	HTSlib high-throughput sequencing library as an R package
rHVDM	Martino Barenco	Hidden Variable Dynamic Modeling
riboSeqR	Thomas J. Hardcastle	Analysis of sequencing data from ribosome profiling experiments.
Ringo	J. Toedling	R Investigation of ChIP-chip Oligoarrays
RIPSeeker	Yue Li	RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
Risa	Alejandra Gonzalez-Beltran, ISA Team	Converting experimental metadata from ISA-tab into Bioconductor data structures
RLMM	Nusrat Rabbee	A Genotype Calling Algorithm for Affymetrix SNP Arrays
Rmagpie	Camille Maumet	MicroArray Gene-expression-based Program In Error rate estimation
RMassBank	RMassBank at Eawag	Workflow to process tandem MS files and build MassBank records
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
RNAinteract	Bernd Fischer	Estimate Pairwise Interactions from multidimensional features
RNAither	Lars Kaderali	Statistical analysis of high-throughput RNAi screens
RNAprobR	Nikos Sidiropoulos	An R package for analysis of massive parallel sequencing based RNA structure probing data
rnaSeqMap	Michal Okoniewski	rnaSeq secondary analyses
RNASeqPower	Terry M Therneau	Sample size for RNAseq studies
RnaSeqSampleSize	Shilin Zhao	RnaSeqSampleSize
RnBeads	Fabian Mueller	RnBeads
Rnits	Dipen P. Sangurdekar	R Normalization and Inference of Time Series data
roar	Elena Grassi	Identify differential APA usage from RNA-seq alignments
ROC	Vince Carey	utilities for ROC, with uarray focus
Roleswitch	Yue Li	Infer miRNA-mRNA interactions using paired expression data from a single sample
Rolexa	Jacques Rougemont	Statistical analysis of Solexa sequencing data
rols	Laurent Gatto	An R interface to the Ontology Lookup Service
ROntoTools	Calin Voichita	R Onto-Tools suite
RPA	Leo Lahti	RPA: Robust Probabilistic Averaging for probe-level analysis
RpsiXML	Jitao David Zhang	R interface to PSI-MI 2.5 files
rpx	Laurent Gatto	R Interface to the ProteomeXchange Repository
Rqc	Welliton Souza	Quality Control Tool for High-Throughput Sequencing Data
rqubic	Jitao David Zhang	Qualitative biclustering algorithm for expression data analysis in R
rRDP	Michael Hahsler	Interface to the RDP Classifier
RRHO	Jonathan Rosenblatt	Inference on agreement between ordered lists
Rsamtools	Bioconductor Package Maintainer	Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
rsbml	Michael Lawrence	R support for SBML, using libsbml
rSFFreader	Matt Settles	rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers
Rsubread	Wei Shi	Rsubread package: high-performance read alignment, quantification and mutation discovery
RSVSim	Christoph Bartenhagen	RSVSim: an R/Bioconductor package for the simulation of structural variations
rTANDEM	Frederic Fournier	Interfaces the tandem protein identification algorithm in R
RTCA	Jitao David Zhang	Open-source toolkit to analyse data from xCELLigence System (RTCA)
RTN	Mauro Castro	Reconstruction of transcriptional networks and analysis of master regulators
RTopper	Luigi Marchionni	This package is designed to perform Gene Set Analysis across multiple genomic platforms
rtracklayer	Michael Lawrence	R interface to genome browsers and their annotation tracks
Rtreemix	Jasmina Bogojeska	Rtreemix: Mutagenetic trees mixture models.
rTRM	Diego Diez	Identification of transcriptional regulatory modules from PPI networks
rTRMui	Diego Diez	A shiny user interface for rTRM
RUVcorr	Saskia Freytag	Removal of unwanted variation for gene-gene correlations and related analysis
RUVnormalize	Laurent Jacob	RUV for normalization of expression array data
RUVSeq	Davide Risso	Remove Unwanted Variation from RNA-Seq Data
RWebServices	Martin Morgan	Expose R functions as web services through Java/Axis/Apache
S4Vectors	Bioconductor Package Maintainer	S4 implementation of vectors and lists
safe	William T. Barry	Significance Analysis of Function and Expression
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.
sangerseqR	Jonathon Hill	Tools for Sanger Sequencing Data in R
SANTA	Alex J. Cornish	Spatial Analysis of Network Associations
sapFinder	Shaohang Xu, Bo Wen	A package for variant peptides detection and visualization in shotgun proteomics.
saps	Daniel Schmolze	Significance Analysis of Prognostic Signatures
savR	R. Brent Calder	Parse and analyze Illumina SAV files
SBMLR	Tomas Radivoyevitch	SBML-R Interface and Analysis Tools
SCAN.UPC	Stephen R. Piccolo	Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
ScISI	Tony Chiang	In Silico Interactome
scsR	Andrea Franceschini, Roger Meier, Christian von Mering	SiRNA correction for seed mediated off-target effect
segmentSeq	Thomas J. Hardcastle	Methods for identifying small RNA loci from high-throughput sequencing data
SELEX	Harmen Bussemaker	Functions for analyzing SELEX-seq data
SemDist	Ian Gonzalez	Information Accretion-based Function Predictor Evaluation
seq2pathway	Xinan Yang with contribution from Lorenzo Pesce and Ana Marija Sokovic	a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data
SeqArray	Xiuwen Zheng	Big Data Management of Genome-wide Sequencing Variants
seqbias	Daniel Jones	Estimation of per-position bias in high-throughput sequencing data
seqCNA	David Mosen-Ansorena	Copy number analysis of high-throughput sequencing cancer data
SeqGSEA	Xi Wang	Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
seqLogo	Oliver Bembom	Sequence logos for DNA sequence alignments
seqPattern	Vanja Haberle	Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences
seqplots	Przemyslaw Stempor	An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
seqTools	Wolfgang Kaisers	Analysis of nucleotide, sequence and quality content on fastq files.
SeqVarTools	Stephanie M. Gogarten, Xiuwen Zheng	Tools for variant data
SGSeq	Leonard Goldstein	Splice event detection and quantification from RNA-seq data
shinyMethyl	Jean-Philippe Fortin	Interactive visualization for Illumina's 450k methylation arrays
shinyTANDEM	Frederic Fournier	Provides a GUI for rTANDEM
ShortRead	Bioconductor Package Maintainer	FASTQ input and manipulation
sigaR	Wessel N. van Wieringen	statistics for integrative genomics analyses in R
SigCheck	Rory Stark	Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
SigFuge	Patrick Kimes	SigFuge
siggenes	Holger Schwender	Multiple testing using SAM and Efron's empirical Bayes approaches
sigPathway	Weil Lai	Pathway Analysis
sigsquared	UnJin Lee	Gene signature generation for functionally validated signaling pathways
SIM	Renee X. de Menezes	Integrated Analysis on two human genomic datasets
SIMAT	Mo R. Nezami Ranjbar	GC-SIM-MS data processing and alaysis tool
SimBindProfiles	Bettina Fischer	Similar Binding Profiles
similaRpeak	Astrid Louise Deschenes	similaRpeak: Metrics to estimate a level of similarity between two ChIP-Seq profiles
simpleaffy	Crispin Miller	Very simple high level analysis of Affymetrix data
simulatorZ	Yuqing Zhang	Simulator for Collections of Independent Genomic Data Sets
sincell	Miguel Juliá, Antonio Rausell	R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
sizepower	Weiliang Qiu	Sample Size and Power Calculation in Micorarray Studies
SJava	Martin Morgan	The Omegahat interface for R and Java
skewr	Ryan Putney	Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
SLGI	Nolwenn Le Meur	Synthetic Lethal Genetic Interaction
SLqPCR	Matthias Kohl	Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH
SMAP	Robin Andersson	A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
SNAGEE	David Venet	Signal-to-Noise applied to Gene Expression Experiments
snapCGH	John Marioni	Segmentation, normalisation and processing of aCGH data.
snm	John D. Storey	Supervised Normalization of Microarrays
SNPchip	Robert Scharpf	Visualizations for copy number alterations
SNPRelate	Xiuwen Zheng	Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
snpStats	David Clayton	SnpMatrix and XSnpMatrix classes and methods
soGGi	Tom Carroll	Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals
SomatiCA	Mengjie Chen	SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing
SomaticSignatures	Julian Gehring	Somatic Signatures
SpacePAC	Gregory Ryslik	Identification of Mutational Clusters in 3D Protein Space via Simulation.
spade	Zach Bjornson	SPADE -- An analysis and visualization tool for Flow Cytometry
specL	Christian Panse	specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
SpeCond	Florence Cavalli	Condition specific detection from expression data
SPEM	Xinyi YANG	S-system parameter estimation method
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
splicegear	Laurent Gautier	splicegear
spliceR	Johannes Waage, Kristoffer Vitting-Seerup	Classification of alternative splicing and prediction of coding potential from RNA-seq data.
spliceSites	Wolfgang Kaisers	Manages align gap positions from RNA-seq data
SplicingGraphs	H. Pages	Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
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
SQUADD	Martial Sankar	Add-on of the SQUAD Software
SRAdb	Jack Zhu	A compilation of metadata from NCBI SRA and tools
sRAP	Charles Warden	Simplified RNA-Seq Analysis Pipeline
sscore	Richard Kennedy	S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
sSeq	Danni Yu	Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
ssize	Gregory R. Warnes	Estimate Microarray Sample Size
SSPA	Maarten van Iterson	General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data
ssviz	Diana Low	A small RNA-seq visualizer and analysis toolkit
STAN	Benedikt Zacher	STrand-specific ANnotation of genomic data
staRank	Juliane Siebourg	Stability Ranking
Starr	Benedikt Zacher	Simple tiling array analysis of Affymetrix ChIP-chip data
STATegRa	David Gomez-Cabrero, Patricia Sebastián-León, Gordon Ball	Classes and methods for multi-omics data integration
stepNorm	Yuanyuan Xiao	Stepwise normalization functions for cDNA microarrays
stepwiseCM	Askar Obulkasim	Stepwise Classification of Cancer Samples using High-dimensional Data Sets
Streamer	Martin Morgan	Enabling stream processing of large files
STRINGdb	Andrea Franceschini	STRINGdb (Search Tool for the Retrieval of Interacting proteins database)
supraHex	Hai Fang	A supra-hexagonal map for analysing tabular omics data
survcomp	Benjamin Haibe-Kains, Markus Schroeder, Catharina Olsen	Performance Assessment and Comparison for Survival Analysis
Sushi	Douglas H Phanstiel	Tools for visualizing genomics data
sva	Jeffrey T. Leek, John D. Storey, W. Evan Johnson	Surrogate Variable Analysis
SVM2CRM	Guidantonio Malagoli Tagliazucchi	SVM2CRM: support vector machine for cis-regulatory elements detections
SwimR	Randy Blakely	SwimR: A Suite of Analytical Tools for Quantification of C. elegans Swimming Behavior
switchBox	Bahman Afsari, Luigi Marchionni	Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm.
synapter	Laurent Gatto and Sebastian Gibb	Label-free data analysis pipeline for optimal identification and quantitation
systemPipeR	Thomas Girke	systemPipeR: NGS workflow and report generation environment
TargetScore	Yue Li	TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information
TargetSearch	Alvaro Cuadros-Inostroza	A package for the analysis of GC-MS metabolite profiling data.
TCC	Jianqiang Sun, Tomoaki Nishiyama	TCC: Differential expression analysis for tag count data with robust normalization strategies
TDARACNE	Zoppoli Pietro	Network reverse engineering from time course data.
TEQC	Manuela Hummel	Quality control for target capture experiments
ternarynet	Matthew N. McCall	Ternary Network Estimation
TFBSTools	Ge Tan	Software package for transcription factor binding site (TFBS) analysis
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
TIN	Bjarne Johannessen	Transcriptome instability analysis
TitanCNA	Gavin Ha, Sohrab P Shah	Subclonal copy number and LOH prediction from whole genome sequencing of tumours
tkWidgets	J. Zhang	R based tk widgets
ToPASeq	Ivana Ihnatova	Package for Topology-based Pathway Analysis of RNASeq data
topGO	Adrian Alexa	topGO: Enrichment analysis for Gene Ontology
TPP	Dorothee Childs	Analyze thermal proteome profiling (TPP) experiments
tracktables	Tom Carroll	Build IGV tracks and HTML reports
trackViewer	Jianhong Ou	A bioconductor package with minimalist design for plotting elegant track layers
tRanslatome	Toma Tebaldi, Erik Dassi	Comparison between multiple levels of gene expression
TransView	Julius Muller	Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets.
triform	Tony Handstad Developer	Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data
trigger	John D. Storey	Transcriptional Regulatory Inference from Genetics of Gene ExpRession
trio	Holger Schwender	Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
triplex	Jiri Hon	Search and visualize intramolecular triplex-forming sequences in DNA
TRONCO	Giulio Caravagna, Alex Graudenzi, Daniele Ramazzotti	TRONCO, a package for TRanslational ONCOlogy
TSCAN	Zhicheng Ji	TSCAN: Tools for Single-Cell ANalysis
tspair	Jeffrey T. Leek	Top Scoring Pairs for Microarray Classification
TSSi	Julian Gehring	Transcription Start Site Identification
TurboNorm	Maarten van Iterson	A fast scatterplot smoother suitable for microarray normalization
tweeDEseq	Juan R Gonzalez	RNA-seq data analysis using the Poisson-Tweedie family of distributions
twilight	Stefanie Scheid	Estimation of local false discovery rate
TypeInfo	Duncan Temple Lang	Optional Type Specification Prototype
UNDO	Niya Wang	Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions
unifiedWMWqPCR	Joris Meys	Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
UniProt.ws	Marc Carlson	R Interface to UniProt Web Services
VanillaICE	Robert Scharpf	A Hidden Markov Model for high throughput genotyping arrays
VariantAnnotation	Valerie Obenchain	Annotation of Genetic Variants
VariantFiltering	Robert Castelo	Filtering of coding and non-coding genetic variants
VariantTools	Michael Lawrence	Tools for Working with Genetic Variants
vbmp	Nicola Lama	Variational Bayesian Multinomial Probit Regression
Vega	Sandro Morganella	An R package for copy number data segmentation
VegaMC	Sandro Morganella	VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer
viper	Mariano J Alvarez	Virtual Inference of Protein-activity by Enriched Regulon analysis
vsn	Wolfgang Huber	Variance stabilization and calibration for microarray data
vtpnet	VJ Carey	variant-transcription factor-phenotype networks
wateRmelon	Leo	Illumina 450 methylation array normalization and metrics
wavClusteR	Federico Comoglio	Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
waveTiling	Kristof De Beuf	Wavelet-Based Models for Tiling Array Transcriptome Analysis
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
xcms	Steffen Neumann	LC/MS and GC/MS Data Analysis
XDE	Robert Scharpf	XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
xmapbridge	Chris Wirth	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
XVector	H. Pages	Representation and manpulation of external sequences
yaqcaffy	Laurent Gatto	Affymetrix expression data quality control and reproducibility analysis
zlibbioc	Bioconductor Package Maintainer	An R packaged zlib-1.2.5

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