Bioconductor Software Packages

Bioconductor version: Release (3.4)

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
ABAEnrichment	Steffi Grote	Gene expression enrichment in human brain regions
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
acde	Juan Pablo Acosta	Artificial Components Detection of Differentially Expressed Genes
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	Yifang Hu, Gordon Smyth, Keith Satterley	GUI for limma package with Affymetrix microarrays
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
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
alpine	Michael Love	alpine
alsace	Ron Wehrens	ALS for the Automatic Chemical Exploration of mixtures
altcdfenvs	Laurent Gautier	alternative CDF environments (aka probeset mappings)
AMOUNTAIN	Dong Li	Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach
ampliQueso	Michal Okoniewski	Analysis of amplicon enrichment panels
AnalysisPageServer	Brad Friedman	A framework for sharing interactive data and plots from R through the web.
anamiR	Ti-Tai Wang	An integrated analysis package of miRNA and mRNA expression data
Anaquin	Ted Wong	Statistical analysis of sequins
AneuFinder	Aaron Taudt	Analysis of Copy Number Variation in Single-Cell-Sequencing Data
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
AnnotationHubData	Bioconductor Package Maintainer	Transform public data resources into Bioconductor Data Structures
annotationTools	Alexandre Kuhn	Annotate microarrays and perform cross-species gene expression analyses using flat file databases.
annotatr	Raymond G. Cavalcante	Annotation of Genomic Regions to Genomic Annotations
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
ASAFE	Qian Zhang	Ancestry Specific Allele Frequency Estimation
ASEB	Likun Wang	Predict Acetylated Lysine Sites
ASGSCA	Hela Romdhani	Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models
ASpli	Estefania Mancini	Analysis of alternative splicing using RNA-Seq
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	Simon Jupp	Gene Expression Atlas query and gene set enrichment package.
attract	Samuel Zimmerman	Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
BaalChIP	Ines de Santiago	BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
BAC	Raphael Gottardo	Bayesian Analysis of Chip-chip experiment
bacon	Maarten van Iterson	Controlling bias and inflation in association studies using the empirical null distribution
BADER	Andreas Neudecker	Bayesian Analysis of Differential Expression in RNA Sequencing Data
BadRegionFinder	Sarah Sandmann	BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
BAGS	Alejandro Quiroz-Zarate	A Bayesian Approach for Geneset Selection
ballgown	Jack Fu	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
BasicSTARRseq	Annika Buerger	Basic peak calling on STARR-seq data
BatchQC	Solaiappan Manimaran	Batch Effects Quality Control Software
BayesKnockdown	William Chad Young	BayesKnockdown: Posterior Probabilities for Edges from Knockdown 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
BBCAnalyzer	Sarah Sandmann	BBCAnalyzer: an R/Bioconductor package for visualizing base counts
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
BgeeDB	Andrea Komljenovic, Frederic Bastian	Annotation and gene expression data retrieval from Bgee database
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
bigmelon	Tyler Gorrie-Stone	Illumina methylation array analysis for large experiments
bigmemoryExtras	Peter M. Haverty	An extension of the bigmemory package with added safety, convenience, and a factor class
bioassayR	Tyler Backman	Cross-target analysis of small molecule bioactivity
Biobase	Bioconductor Package Maintainer	Biobase: Base functions for Bioconductor
biobroom	John D. Storey and Andrew J. Bass	Turn Bioconductor objects into tidy data frames
bioCancer	Karim Mezhoud	Interactive Multi-Omics Cancers Data Visualization and Analysis
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, CRAN, and github 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
BiocWorkflowTools	Mike Smith	Tools to aid the development of Bioconductor Workflow packages
bioDist	Bioconductor Package Maintainer	Different distance measures
biomaRt	Steffen Durinck	Interface to BioMart databases (e.g. Ensembl, COSMIC, Wormbase and Gramene)
biomformat	Paul J. McMurdie	An interface package for the BIOM file format
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
BioQC	Jitao David Zhang	Detect tissue heterogeneity in expression profiles with gene sets
BioSeqClass	Li Hong	Classification for Biological Sequences
biosigner	Philippe Rinaudo, Etienne Thevenot	Signature discovery from omics data
Biostrings	H. Pagès	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	Michael Lawrence	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), undirected 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.
BPRMeth	Chantriolnt-Andreas Kapourani	Model higher-order methylation profiles
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	Egon Willighagen	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. Pagès	Infrastructure for Biostrings-based genome data packages and support for efficient SNP representation
bsseq	Kasper Daniel Hansen	Analyze, manage and store bisulfite sequencing data
BubbleTree	Todd Creasy, Wei Zhu	BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
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	Steffen Neumann	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
CancerInSilico	Thomas D. Sherman, Elana J. Fertig	An R interface for computational modeling of tumor progression
CancerMutationAnalysis	Simina M. Boca	Cancer mutation analysis
CancerSubtypes	Taosheng Xu	Cancer subtypes identification, validation and visualization based on genomic data
CAnD	Caitlin McHugh	Perform Chromosomal Ancestry Differences (CAnD) Analyses
caOmicsV	Henry Zhang	Visualization of multi-dimentional cancer genomics data
Cardinal	Kylie A. 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
CausalR	Glyn Bradley, Steven Barrett, Bhushan Bonde	Causal Reasoning Methods
ccmap	Alex Pickering	Combination Connectivity Mapping
CCPROMISE	Xueyuan Cao	PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data
ccrepe	Emma Schwager,Craig Bielski, George Weingart	ccrepe_and_nc.score
cellGrowth	Julien Gagneur	Fitting cell population growth models
cellHTS2	Joseph Barry	Analysis of cell-based screens - revised version of cellHTS
cellity	Tomislav Ilicic	Quality Control for Single-Cell RNA-seq Data
CellMapper	Brad Nelms	Predict genes expressed selectively in specific cell types
CellNOptR	T.Cokelaer	Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.
cellTree	David duVerle	Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
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	Yuan Tian	Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
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
Chicago	Mikhail Spivakov	CHiCAGO: Capture Hi-C Analysis of Genomic Organization
chimera	Raffaele A Calogero	A package for secondary analysis of fusion products
ChIPComp	Li Chen	Quantitative comparison of multiple ChIP-seq datasets
chipenrich	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 is a R package for drawing the schemes of karyotypes in the linear and circular fashion.
ChromHeatMap	Tim F. Rayner	Heat map plotting by genome coordinate
chromPlot	Karen Y. Orostica	Global visualization tool of genomic data
chromstaR	Aaron Taudt	Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
CHRONOS	Panos Balomenos	CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
CINdex	Yuriy Gusev	Chromosome Instability Index
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.
clustComp	Aurora Torrente	Clustering Comparison Package
clusterExperiment	Elizabeth Purdom	Compare clusterings for single-cell sequencing
clusterProfiler	Guangchuang Yu	statistical analysis and visualization of functional profiles for genes and gene clusters
ClusterSignificance	Jason T Serviss	The ClusterSignificance package provides tools to assess if clusters have a separation different from random or permuted data
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
CNPBayes	Jacob Carey	Bayesian mixture models for copy number polymorphisms
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
CNVPanelizer	Thomas Wolf	Reliable CNV detection in targeted sequencing applications
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	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
CONFESS	Diana LOW	Cell OrderiNg by FluorEScence Signal
ConsensusClusterPlus	Matt Wilkerson	ConsensusClusterPlus
consensusSeekeR	Astrid Louise Deschenes	Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
contiBAIT	Kieran O'Neill	Improves Early Build Genome Assemblies using Strand-Seq Data
conumee	Volker Hovestadt	Enhanced copy-number variation analysis using Illumina DNA 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.
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
CountClust	Kushal Dey	Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
covEB	C. Pacini	Empirical Bayes estimate of block diagonal covariance matrices
CoverageView	Ernesto Lowy	Coverage visualization package for R
covRNA	Lara Urban	Multivariate Analysis of Transcriptomic Data
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
crisprseekplus	Alper Kucukural	crisprseekplus
CrispRVariants	Helen Lindsay	Tools for counting and visualising mutations in a target location
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
crossmeta	Alex Pickering	Cross Platform Meta-Analysis of Microarray Data
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.
ctsGE	Michal Sharabi-Schwager	Clustering of Time Series Gene Expression data
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.
CVE	Andreas Mock	Cancer Variant Explorer
cycle	Matthias Futschik	Significance of periodic expression pattern in time-series data
cytofkit	Jinmiao Chen, Hao Chen	cytofkit: an integrated mass cytometry data analysis pipeline
CytoML	Mike Jiang	GatingML interface for openCyto
dada2	Benjamin Callahan	Accurate, high-resolution sample inference from amplicon sequencing data
dagLogo	Jianhong Ou	dagLogo
daMA	Jobst Landgrebe	Efficient design and analysis of factorial two-colour microarray data
DAPAR	Samuel Wieczorek	Tools for the Differential Analysis of Proteins Abundance with R
DART	Charles Shijie Zheng	Denoising Algorithm based on Relevance network Topology
DBChIP	Kun Liang	Differential Binding of Transcription Factor with ChIP-seq
dcGSA	Jiehuan sun	Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
DChIPRep	Bernd Klaus	DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
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
debrowser	Alper Kucukural	debrowser: Interactive Differential Expresion Analysis Browser
DECIPHER	Erik Wright	Tools for curating, analyzing, and manipulating biological sequences
DeconRNASeq	Ting Gong	Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
DEDS	Yuanyuan Xiao	Differential Expression via Distance Summary for Microarray Data
DeepBlueR	Felipe Albrecht, Markus List	DeepBlueR
deepSNV	Moritz Gerstung	Detection of subclonal SNVs in deep sequencing data.
DEFormats	Andrzej Oleś	Differential gene expression data formats converter
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
DeMAND	Jung Hoon Woo, Mariano Alvarez	DeMAND
derfinder	Leonardo Collado-Torres	Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
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
destiny	Philipp Angerer	Creates diffusion maps
DEsubs	Aristidis G. Vrahatis and Panos Balomenos	DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
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
DiffLogo	Hendrik Treutler	DiffLogo: A comparative visualisation of sequence motifs
diffloop	Caleb Lareau	Identifying differential DNA loops from chromatin topology data
diggit	Mariano J Alvarez	Inference of Genetic Variants Driving Cellular Phenotypes
Director	Katherine Icay	A dynamic visualization tool of multi-level data
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	Methylation array and sequencing spatial analysis methods
DMRforPairs	Martin Rijlaarsdam	DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
DNABarcodes	Tilo Buschmann	A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments
DNAcopy	Venkatraman E. Seshan	DNA copy number data analysis
DNAshapeR	Tsu-Pei Chiu	High-throughput prediction of DNA shape features
domainsignatures	Florian Hahne	Geneset enrichment based on InterPro domain signatures
doppelgangR	Levi Waldron	Identify likely duplicate samples from genomic or meta-data
DOQTL	Daniel Gatti	Genotyping and QTL Mapping in DO Mice
DOSE	Guangchuang Yu	Disease Ontology Semantic and Enrichment analysis
DRIMSeq	Malgorzata Nowicka	Differential splicing and sQTL analyses with Dirichlet-multinomial model in RNA-Seq
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
dSimer	Peng Ni	Integration of Disease Similarity Methods
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
dupRadar	Sergi Sayols, Holger Klein	Assessment of duplication rates in RNA-Seq datasets
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
EBSEA	Arfa Mehmood	Exon Based Strategy for Expression Analysis of genes
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, Andrew J. Bass	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
eegc	Xiaoyuan Zhou	Engineering Evaluation by Gene Categorization (eegc)
EGAD	Sara Ballouz	Extending guilt by association by degree
EGSEA	Monther Alhamdoosh	Ensemble of Gene Set Enrichment Analyses
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
ELMER	Simon Coetzee	Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
EMDomics	Sadhika Malladi and Daniel Schmolze	Earth Mover's Distance for Differential Analysis of Genomics Data
EmpiricalBrownsMethod	David Gibbs	Uses Brown's method to combine p-values from dependent tests
ENCODExplorer	Charles Joly Beauparlant	A compilation of ENCODE metadata
ENmix	Zongli Xu	Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
EnrichedHeatmap	Zuguang Gu	Making Enriched Heatmaps
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	Bioconductor Package Maintainer	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
epivizrData	Hector Corrada Bravo	Data Management API for epiviz interactive visualization app
epivizrServer	Hector Corrada Bravo	WebSocket server infrastructure for epivizr apps and packages
epivizrStandalone	Hector Corrada Bravo	Run Epiviz Interactive Genomic Data Visualization App within R
erccdashboard	Sarah Munro	Assess Differential Gene Expression Experiments with ERCC Controls
erma	VJ Carey	epigenomic road map adventures
esetVis	Laure Cougnaud	Visualizations of expressionSet Bioconductor object
eudysbiome	Xiaoyuan Zhou	Cartesian plot and contingency test on 16S Microbial data
EWCE	Nathan Skene	Expression Weighted Celltype Enrichment
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	Lin Zhang, Lian Liu, Jia Meng	exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis
ExperimentHub	Bioconductor Package Maintainer	Client to access ExperimentHub resources
ExperimentHubData	Bioconductor Package Maintainer	Add resources to ExperimentHub
explorase	Michael Lawrence	GUI for exploratory data analysis of systems biology data
ExpressionAtlas	Maria Keays	Download datasets from EMBL-EBI Expression Atlas
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
FamAgg	Johannes Rainer	Pedigree Analysis and Familial Aggregation
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
fCCAC	Pedro Madrigal	functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
fCI	Shaojun Tang	f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics
fdrame	Effi Kenigsberg	FDR adjustments of Microarray Experiments (FDR-AME)
FEM	Zhen Yang	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
fgsea	Alexey Sergushichev	Fast Gene Set Enrichment Analysis
FindMyFriends	Thomas Lin Pedersen	Microbial Comparative Genomics in R
FISHalyseR	Karesh Arunakirinathan, Andreas Heindl	FISHalyseR a package for automated FISH quantification
FitHiC	Ruyu Tan	Confidence estimation for intra-chromosomal contact maps
flagme	Mark Robinson, Riccardo Romoli	Analysis of Metabolomics GC/MS Data
flipflop	Elsa Bernard	Fast lasso-based isoform prediction as a flow problem
flowAI	Gianni Monaco	Automatic and interactive quality control for flow cytometry data
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
flowPloidy	Tyler Smith	Analyze flow cytometer data to determine sample ploidy
flowPlots	N. Hawkins	flowPlots: analysis plots and data class for gated flow cytometry data
flowQ	Mike Jiang	Quality control for flow cytometry
flowQB	Josef Spidlen	Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic 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	Infrastructure for representing and interacting with the gated cytometry
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
FunChIP	Alice Parodi	Clustering and Alignment of ChIP-Seq peaks based on their shapes
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.
GAprediction	Jon Bohlin	Prediction of gestational age with Illumina HumanMethylation450 data
garfield	Valentina Iotchkova	GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
gaucho	Alex Murison, Christopher Wardell	Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering
gcatest	Wei Hao, John D. Storey	Genotype Conditional Association TEST
gCMAP	Thomas Sandmann	Tools for Connectivity Map-like analyses
gCMAPWeb	Thomas Sandmann	A web interface for gene-set enrichment analyses
gCrisprTools	Russell Bainer	Suite of Functions for Pooled Crispr Screen QC and Analysis
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
GEM	Hong Pan	GEM: fast association study for the interplay of Gene, Environment and Methylation
genArise	IFC Development Team	Microarray Analysis tool
genbankr	Gabriel Becker	Parsing GenBank files into semantically useful objects
GENE.E	Joshua Gould	Interact with GENE-E from R
GeneAnswers	Lei Huang and Gang Feng	Integrated Interpretation of Genes
geneAttribution	Arthur Wuster	Identification of candidate genes associated with genetic variation
GeneBreak	Evert van den Broek	Gene Break Detection
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	Computation of Gene Expression-Based Signatures in Breast Cancer
GeneGA	Zhenpeng Li	Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
GeneGeneInteR	Mathieu Emily, Magalie Houee-Bigot	Tools for Testing Gene-Gene Interaction at the Gene Level
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
geneplast	Mauro Castro	Evolutionary and plasticity analysis based on orthologous groups distribution
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
geneXtendeR	Bohdan Khomtchouk	Optimal Gene Extensions From Histone Modification ChIP-seq Data
genoCN	Wei Sun	genotyping and copy number study tools
GenoGAM	Georg Stricker	A GAM based framework for analysis of ChIP-Seq data
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 and variables defined along a genome
GenomicTuples	Peter Hickey	Representation and Manipulation of Genomic Tuples
Genominator	James Bullard	Analyze, manage and store genomic data
genoset	Peter M. Haverty	A RangedSummarizedExperiment with methods for copy number analysis
genotypeeval	Jennifer Tom	QA/QC of a gVCF or VCF file
genphen	Simo Kitanovski	A tool for quantification of associations between genotypes and phenotypes with statistical learning techniques such as random forests and support vector machines as well as with Bayesian inference using hierarchical models
GenRank	Chakravarthi Kanduri	Candidate gene prioritization based on convergent evidence
GenVisR	Zachary Skidmore	Genomic Visualizations in R
GEOmetadb	Jack Zhu	A compilation of metadata from NCBI GEO
GEOquery	Sean Davis	Get data from NCBI Gene Expression Omnibus (GEO)
GEOsearch	Zhicheng Ji	GEOsearch
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	Michael Lawrence	Visualization tools for genomic data.
ggcyto	Mike Jiang	Visualize Cytometry data with ggplot
GGtools	VJ Carey	software and data for analyses in genetics of gene expression
ggtree	Guangchuang Yu	an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
girafe	J. Toedling	Genome Intervals and Read Alignments for Functional Exploration
GLAD	Philippe Hupe	Gain and Loss Analysis of DNA
Glimma	Shian Su	Interactive HTML graphics
GlobalAncova	Manuela Hummel	Calculates a global test for differential gene expression between groups
globalSeq	Armin Rauschenberger	Testing for association between RNA-Seq and high-dimensional data
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
GMRP	Yuan-De Tan	GWAS-based Mendelian Randomization and Path Analyses
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
GOpro	Lidia Chrabaszcz	Find the most characteristic gene ontology terms for groups of human genes
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, Anthony Hawkins	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
GRmetrics	Nicholas Clark	Calculate growth-rate inhibition (GR) metrics
groHMM	Anusha Nagari, Venkat Malladi, Tulip Nandu, W. Lee Kraus	GRO-seq Analysis Pipeline
GSALightning	Billy Heung Wing Chang	Fast Permutation-based Gene Set Analysis
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
GUIDEseq	Lihua Julie Zhu	GUIDE-seq analysis pipeline
Guitar	Jia Meng	Guitar
Gviz	Florian Hahne	Plotting data and annotation information along genomic coordinates
gwascat	VJ Carey	representing and modeling data in the EMBL-EBI 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
Harman	Jason Ross	The removal of batch effects from datasets using a PCA and constrained optimisation based technique
Harshlight	Maurizio Pellegrino	A "corrective make-up" program for microarray chips
HCsnip	Askar Obulkasim	Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree
HDF5Array	Hervé Pagès	An array-like container for convenient access and manipulation of HDF5 datasets
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
HelloRanges	Michael Lawrence	Introduce *Ranges to bedtools users
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
hierGWAS	Laura Buzdugan	Asessing statistical significance in predictive GWA studies
HilbertCurve	Zuguang Gu	Making 2D Hilbert Curve
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, 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
iCARE	Bill Wheeler	A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)
Icens	Bioconductor Package Maintainer	NPMLE for Censored and Truncated Data
iCheck	Weiliang Qiu	QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression 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
iCOBRA	Charlotte Soneson	Comparison and Visualization of Ranking and Assignment Methods
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
iGC	Liang-Bo Wang	An integrated analysis package of Gene expression and Copy number alteration
IHW	Nikos Ignatiadis	Independent Hypothesis Weighting
illuminaio	Kasper Daniel Hansen	Parsing Illumina Microarray Output Files
imageHTS	Joseph Barry	Analysis of high-throughput microscopy-based screens
Imetagene	Audrey Lemacon	A graphical interface for the metagene package
ImmuneSpaceR	Renan Sauteraud	A Thin Wrapper around the ImmuneSpace Database
immunoClust	Till Soerensen	immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
IMPCdata	Jeremy Mason	Retrieves data from IMPC database
ImpulseDE	Jil Sander, Nir Yosef	Detection of DE genes in time series data using impulse models
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
INSPEcT	Stefano de Pretis	Analysis of 4sU-seq and RNA-seq time-course data
intansv	Wen Yao	Integrative analysis of structural variations
InteractionSet	Aaron Lun	Base Classes for Storing Genomic Interaction Data
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
IONiseR	Mike Smith	Quality Assessment Tools for Oxford Nanopore MinION 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
IPO	Thomas Riebenbauer	Automated Optimization of XCMS Data Processing parameters
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
ISoLDE	Christelle Reynès	Integrative Statistics of alleLe Dependent Expression
isomiRs	Lorena Pantano	Analyze isomiRs and miRNAs from small RNA-seq
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
joda	Ewa Szczurek	JODA algorithm for quantifying gene deregulation using knowledge
JunctionSeq	Stephen Hartley	JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
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
KEGGlincs	Shana White	Visualize all edges within a KEGG pathway and overlay LINCS data [option]
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
kimod	M L Zingaretti	A k-tables approach to integrate multiple Omics-Data
lapmix	Yann Ruffieux	Laplace Mixture Model in Microarray Experiments
LBE	Cyril Dalmasso	Estimation of the false discovery rate.
ldblock	VJ Carey	data structures for linkage disequilibrium measures in populations
LEA	Eric Frichot	LEA: an R package for Landscape and Ecological Association Studies
LedPred	Aitor Gonzalez	Learning from DNA to Predict Enhancers
les	Julian Gehring	Identifying Differential Effects in Tiling Microarray Data
lfa	Wei Hao, John D. Storey	Logistic Factor Analysis for Categorical Data
limma	Gordon Smyth	Linear Models for Microarray Data
limmaGUI	Yifang Hu, Gordon Smyth, Keith Satterley	GUI for limma package with two color microarrays
LINC	Manuel Goepferich	co-expression of lincRNAs and protein-coding genes
Linnorm	Ken Shun Hang Yip	Linear model and normality based transformation method (Linnorm)
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
LOBSTAHS	James Collins	Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
logicFS	Holger Schwender	Identification of SNP Interactions
logitT	Tobias Guennel	logit-t Package
lol	Yinyin Yuan	Lots Of Lasso
LOLA	Nathan Sheffield	Location overlap analysis for enrichment of genomic ranges
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	Lars Kaderali	Linear Programming Model for Network Inference
lpsymphony	Vladislav Kim	Symphony integer linear programming solver in R
lumi	Pan Du, Lei Huang, Gang Feng	BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
LVSmiRNA	Stefano Calza	LVS normalization for Agilent miRNA data
LymphoSeq	David Coffey	Analyze high-throughput sequencing of T and B cell receptors
M3D	Tom Mayo	Identifies differentially methylated regions across testing groups
M3Drop	Tallulah Andrews	Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
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
MADSEQ	Yu Kong	Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
maftools	Anand Mayakonda	Summarize, Analyze and Visualize MAF files
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 Gene Expression 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
MAST	Andrew McDavid	Model-based Analysis of Single Cell Transcriptomics
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
matter	Kylie A. Bemis	A framework for rapid prototyping with binary data on disk
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
MBttest	Yuan-De Tan	Multiple Beta t-Tests
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
MEAL	Carlos Ruiz	Perform methylation analysis
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
Mergeomics	Zeyneb Kurt	Integrative network analysis of omics data
MeSHDbi	Koki Tsuyuzaki	DBI to construct MeSH-related package from sqlite file
meshes	Guangchuang Yu	MeSH Enrichment and Semantic analyses
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
MetaboSignal	Andrea Rodriguez-Martinez, Rafael Ayala	MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
metaCCA	Anna Cichonska	Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
metagene	Charles Joly Beauparlant	A package to produce metagene plots
metagenomeFeatures	Nathan D. Olson	Exploration of marker-gene sequence taxonomic annotations
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.
MetCirc	Thomas Naake	A workflow to analyse and visualise metabolomics data
MethPed	Helena Carén	A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
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, Lei Huang, Gang Feng	DNA methylation data analysis and visualization
MethylAid	M. van Iterson	Visual and interactive quality control of large Illumina DNA Methylation array data sets
methylKit	Altuna Akalin	DNA methylation analysis from high-throughput bisulfite sequencing results
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
MGFR	Khadija El Amrani	Marker Gene Finder in RNA-seq 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 Infinium DNA 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
miRcomp	Matthew N. McCall	Tools to assess and compare miRNA expression estimatation methods
mirIntegrator	Diana Diaz	Integrating microRNA expression into signaling pathways for pathway analysis
miRLAB	Thuc Duy Le	Dry lab for exploring miRNA-mRNA relationships
miRNAmeConverter	Stefan J. Haunsberger	Convert miRNA Names to Different miRBase Versions
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	Analysing Illumina HumanMethylation BeadChip 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
MMDiff2	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
MODA	Dong Li	MODA: MOdule Differential Analysis for weighted gene co-expression network
mogsa	Chen Meng	Multiple omics data integrative clustering and gene set analysis
monocle	Cole Trapnell	Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
MoonlightR	Antonio Colaprico, Catharina Olsen	Identify oncogenes and tumor suppressor genes from omics data
MoPS	Philipp Eser	MoPS - Model-based Periodicity Screening
mosaics	Dongjun Chung	MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
motifbreakR	Simon Gert Coetzee	A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites
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
msPurity	Thomas N. Lawson	Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
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
MultiAssayExperiment	Marcel Ramos	Create Classes and Functions for Managing Multiple Assays on Sets of Samples
multiClust	Nathan Lawlor	multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
MultiDataSet	Carlos Ruiz-Arenas	Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and MethylationSet
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
MutationalPatterns	Francis Blokzijl, Roel Janssen	Studying patterns in base substitution catalogues
MVCClass	Elizabeth Whalen	Model-View-Controller (MVC) Classes
mvGST	John R. Stevens	Multivariate and directional gene set testing
mygene	Adam Mark, Cyrus Afrasiabi, Chunlei Wu	Access MyGene.Info_ services
myvariant	Adam Mark, Chunlei Wu	Accesses MyVariant.info variant query and annotation 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)
NanoStringDiff	hong wang	Differential Expression Analysis of NanoString nCounter 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
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
netprioR	Fabian Schmich	A model for network-based prioritisation of genes
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	Valeriia Sherina	Non-detects in qPCR data
normalize450K	Jonathan Alexander Heiss	Preprocessing of Illumina Infinium 450K data
NormqPCR	James Perkins	Functions for normalisation of RT-qPCR data
normr	Johannes Helmuth	Normalization and difference calling in ChIP-seq 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
nucleoSim	Astrid Deschenes	Generate synthetic nucleosome maps
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
odseq	José Jiménez	Outlier detection in multiple sequence alignments
OGSA	Michael F. Ochs	Outlier Gene Set Analysis
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
OncoScore	Daniele Ramazzotti	A tool to identify potentially oncogenic genes
OncoSimulR	Ramon Diaz-Uriarte	Forward Genetic Simulation of Cancer Progression with Epistasis
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
OperaMate	Chenglin Liu	An R package of Data Importing, Processing and Analysis for Opera High Content Screening System
oposSOM	Henry Loeffler-Wirth	Comprehensive analysis of transciptome data
oppar	Soroor Hediyeh zadeh	Outlier profile and pathway analysis in R
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
Oscope	Ning Leng	Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
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	Joseph N. Paulson, 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
PanVizGenerator	Thomas Lin Pedersen	Generate PanViz visualisations from your pangenome
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
Path2PPI	Oliver Philipp	Prediction of pathway-related protein-protein interaction networks
pathifier	Assif Yitzhaky	Quantify deregulation of pathways in cancer
PathNet	Jason B. Smith	An R package for pathway analysis using topological information
PathoStat	Solaiappan Manimaran	PathoStat Statistical Microbiome Analysis Package
pathRender	Vince Carey	Render molecular pathways
pathVar	Samuel Zimmerman	Methods to Find Pathways with Significantly Different Variability
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
pbcmc	Cristobal Fresno	Permutation-Based Confidence for Molecular Classification
pcaExplorer	Federico Marini	Interactive Visualization of RNA-seq Data Using a Principal Components Approach
pcaGoPromoter	Morten Hansen	pcaGoPromoter is used to analyze DNA micro array data
pcaMethods	Henning Redestig	A collection of PCA methods
PCAN	Matthew Page and Patrice Godard	Phenotype Consensus ANalysis (PCAN)
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.
PGA	Bo Wen, Shaohang Xu	An package for identification of novel peptides by customized database derived from RNA-Seq
PGSEA	Karl Dykema	Parametric Gene Set Enrichment Analysis
PharmacoGx	Benjamin Haibe-Kains	Analysis of Large-Scale Pharmacogenomic Data
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	Jeremy Mason	Statistical analysis of phenotypic data
philr	Justin Silverman	Phylogenetic partitioning based ILR transform for metagenomics data
phyloseq	Paul J. McMurdie	Handling and analysis of high-throughput microbiome census data
Pi	Hai Fang	Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level
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
Pigengene	Habil Zare	Infers biological signatures from gene expression data
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	Jack Fu, 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
pqsfinder	Jiri Hon	Identification of potential quadruplex forming sequences
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
Prize	Daryanaz Dargahi	Prize: an R package for prioritization estimation based on analytic hierarchy process
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).
proFIA	Alexis Delabriere	Preprocessing of FIA-HRMS data
profileScoreDist	Paal O. Westermark	Profile score distributions
pRoloc	Laurent Gatto	A unifying bioinformatics framework for spatial proteomics
pRolocGUI	Laurent Gatto, Lisa M Breckels	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
Prostar	Samuel Wieczorek	Provides a GUI for DAPAR
prot2D	Sebastien Artigaud	Statistical Tools for volume data from 2D Gel Electrophoresis
proteinProfiles	Julian Gehring	Protein Profiling
ProteomicsAnnotationHubData	Laurent Gatto	Transform public proteomics data resources into Bioconductor Data Structures
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.
psichomics	Nuno Saraiva-Agostinho	Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
PSICQUIC	Paul Shannon	Proteomics Standard Initiative Common QUery InterfaCe
psygenet2r	Alba Gutierrez-Sacristan	psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
puma	Xuejun Liu	Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
PureCN	Markus Riester	Copy number calling and SNV classification using targeted short read sequencing
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
qsea	Matthias Lienhard	IP-seq data analysis and vizualization
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
QuaternaryProd	Carl Tony Fakhry	Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
QUBIC	Yu Zhang	An R package for qualitative biclustering in support of gene co-expression analyses
qusage	Christopher Bolen	qusage: Quantitative Set Analysis for Gene Expression
qvalue	John D. Storey, Andrew J. Bass	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
R4RNA	Daniel Lai	An R package for RNA visualization and analysis
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	Francesco Del Carratore	Rank Product method for identifying differentially expressed genes with application in meta-analysis
RareVariantVis	Tomasz Stokowy	Visualization of rare variants in whole genome sequencing data
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
RCAS	Bora Uyar	RNA Centric Annotation System
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
rCGH	Frederic Commo	Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
Rchemcpp	Guenter Klambauer	Similarity measures for chemical compounds
RchyOptimyx	Adrin Jalali, Nima Aghaeepour	Optimyzed Cellular Hierarchies for Flow Cytometry
Rcpi	Nan Xiao	Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
RCy3	Tanja Muetze, Georgi Kolishovski, Paul Shannon	Display and manipulate graphs in Cytoscape >= 3.3.0
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.
rDGIdb	Thomas Thurnherr	R Wrapper for DGIdb
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
readat	Richard Cotton	Functionality to Read and Manipulate SomaLogic ADAT files
ReadqPCR	James Perkins	Read qPCR data
reb	Karl J. Dykema	Regional Expression Biases
recount	Leonardo Collado-Torres	Explore and download data from the recount project
recoup	Panagiotis Moulos	An R package for the creation of complex genomic profile plots
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 or PDF reports for a set of genomic regions or DESeq2/edgeR results
regsplice	Lukas M. Weber	Lasso-Based Methods for Detection of Differential Exon Usage
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
RGraph2js	Stephane Cano	Convert a Graph into a D3js Script
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	Bioconductor Package Maintainer	HTSlib high-throughput sequencing library as an R package
rHVDM	Martino Barenco	Hidden Variable Dynamic Modeling
RiboProfiling	A. Popa	Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
riboSeqR	Thomas J. Hardcastle	Analysis of sequencing data from ribosome profiling experiments
RImmPort	Ravi Shankar	RImmPort: Enabling Ready-for-analysis Immunology Research Data
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	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
rnaseqcomp	Mingxiang Teng	Benchmarks for RNA-seq Quantification Pipelines
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
rols	Laurent Gatto	An R interface to the Ontology Lookup Service
ROntoTools	Calin Voichita	R Onto-Tools suite
ropls	Etienne A. Thevenot	PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
ROTS	Fatemeh Seyednasrollah	Reproducibility-Optimized Test Statistic
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	Subread sequence alignment for R
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)
RTCGA	Marcin Kosinski	The Cancer Genome Atlas Data Integration
RTCGAToolbox	Mehmet Kemal Samur	A new tool for exporting TCGA Firehose data
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
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.
savR	R. Brent Calder	Parse and analyze Illumina SAV files
SBMLR	Tomas Radivoyevitch	SBML-R Interface and Analysis Tools
SC3	Vladimir Kiselev	Single-Cell Consensus Clustering
SCAN.UPC	Stephen R. Piccolo	Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
scater	Davis McCarthy	Single-cell analysis toolkit for gene expression data in R
scde	Jean Fan	Single Cell Differential Expression
ScISI	Tony Chiang	In Silico Interactome
scran	Aaron Lun	Methods for Single-Cell RNA-Seq Data Analysis
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
SEPA	Zhicheng Ji	SEPA
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 Whole-genome Sequence Variant Calls
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, Adrienne Stilp	Tools for variant data
sevenbridges	Nan Xiao	Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
SGSeq	Leonard Goldstein	Splice event prediction and quantification from RNA-seq data
shinyMethyl	Jean-Philippe Fortin	Interactive visualization for Illumina methylation arrays
shinyTANDEM	Frederic Fournier	Provides a GUI for rTANDEM
ShortRead	Bioconductor Package Maintainer	FASTQ input and manipulation
SICtools	Xiaobin Xing	Find SNV/Indel differences between two bam files with near relationship
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
sights	Elika Garg	Statistics and dIagnostic Graphs for HTS
signeR	Renan Valieris	Empirical Bayesian approach to mutational signature discovery
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	Metrics to estimate a level of similarity between two ChIP-Seq profiles
SIMLR	Daniele Ramazzotti	SIMLR: Single-cell Interpretation via Multi-kernel LeaRning
simpleaffy	Crispin Miller	Very simple high level analysis of Affymetrix data
simulatorZ	Yuqing Zhang	Simulator for Collections of Independent Genomic Data Sets
sincell	Miguel Julia, Antonio Rausell	R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
SISPA	Bhakti Dwivedi	SISPA: Method for Sample Integrated Set Profile Analysis
sizepower	Weiliang Qiu	Sample Size and Power Calculation in Micorarray Studies
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
SMITE	Neil Ari Wijetunga, Andrew Damon Johnston	Significance-based Modules Integrating the Transcriptome and Epigenome
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
SNPediaR	David Montaner	Query data from SNPedia
SNPhood	Christian Arnold	SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
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
SomaticSignatures	Julian Gehring	Somatic Signatures
SpacePAC	Gregory Ryslik	Identification of Mutational Clusters in 3D Protein Space via Simulation.
specL	Christian Panse, Witold E. Wolski	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
SpidermiR	Claudia Cava	SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data
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	A bioconductor package for exploration of alignment gap positions from RNA-seq data
SplicingGraphs	H. Pagès	Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
splineTimeR	Herbert Braselmann	Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
SPLINTER	Diana Low	Splice Interpreter Of Transcripts
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
SRGnet	Isar Nassiri	SRGnet An R package for studying synergistic response genes from transcriptomics data
sscore	Richard Kennedy	S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
sscu	Yu Sun	Strength of Selected Codon Usage
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	The genomic STate ANnotation package
staRank	Juliane Siebourg	Stability Ranking
StarBioTrek	Claudia Cava	StarBioTrek
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
statTarget	Hemi Luan	Statistical Analysis of Metabolite Profile
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	Alexander Roth	STRINGdb (Search Tool for the Retrieval of Interacting proteins database)
subSeq	Andrew J. Bass, John D. Storey	Subsampling of high-throughput sequencing count data
SummarizedExperiment	Bioconductor Package Maintainer	SummarizedExperiment container
supraHex	Hai Fang	supraHex: 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
SVAPLSseq	Sutirtha Chakraborty	SVAPLSseq-An R package to adjust for the hidden factors of variability in differential gene expression studies based on RNAseq data
SVM2CRM	Guidantonio Malagoli Tagliazucchi	SVM2CRM: support vector machine for cis-regulatory elements detections
SWATH2stats	Peter Blattmann	Transform and Filter SWATH Data for Statistical Packages
SwathXtend	Jemma Wu	SWATH extended library generation and satistical data analysis
SwimR	Randy Blakely	SwimR: A Suite of Analytical Tools for Quantification of C. elegans Swimming Behavior
switchBox	Bahman Afsari, Luigi Marchionni, Wikum Dinalankara	Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
switchde	Kieran Campbell	Switch-like differential expression across single-cell trajectories
synapter	Laurent Gatto and Sebastian Gibb	Label-free data analysis pipeline for optimal identification and quantitation
synergyfinder	Liye He	Calculate and Visualize Synergy Scores for Drug Combinations
synlet	Chunxuan Shao	Hits Selection for Synthetic Lethal RNAi Screen Data
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
TarSeqQC	Gabriela Merino	TARgeted SEQuencing Experiment Quality Control
TCC	Jianqiang Sun, Tomoaki Nishiyama	TCC: Differential expression analysis for tag count data with robust normalization strategies
TCGAbiolinks	Antonio Colaprico, Tiago Chedraoui Silva	TCGAbiolinks: An R/Bioconductor package for integrative analysis with TCGA data
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
tofsims	Lorenz Gerber	Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
ToPASeq	Ivana Ihnatova	Package for Topology-based Pathway Analysis of RNASeq data
topGO	Adrian Alexa	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 drawing elegant tracks or lollipop plot
transcriptR	Armen R. Karapetyan	An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
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
traseR	li chen	GWAS trait-associated SNP enrichment analyses in genomic intervals
triform	Thomas Carroll	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	BIMIB Group	TRONCO, an R 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
TVTB	Kevin Rue-Albrecht	TVTB: The VCF Tool Box
tweeDEseq	Juan R Gonzalez	RNA-seq data analysis using the Poisson-Tweedie family of distributions
twilight	Stefanie Scheid	Estimation of local false discovery rate
tximport	Michael Love	Import and summarize transcript-level estimates for gene-level analysis
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	Bioconductor Package Maintainer	R Interface to UniProt Web Services
Uniquorn	'Raik Otto'	Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
uSORT	Hao Chen	uSORT: A self-refining ordering pipeline for gene selection
VanillaICE	Robert Scharpf	A Hidden Markov Model for high throughput genotyping arrays
variancePartition	Gabriel E. Hoffman	Quantify and interpret divers of variation in multilevel gene expression experiments
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
XBSeq	Yuanhang Liu	Test for differential expression for RNA-seq data
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	Hervé Pagès	Representation and manpulation of external sequences
yamss	Leslie Myint	Tools for high-throughput metabolomics
YAPSA	Daniel Huebschmann	Yet Another Package for Signature Analysis
yaqcaffy	Laurent Gatto	Affymetrix expression data quality control and reproducibility analysis
yarn	Joseph N Paulson	YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
zlibbioc	Bioconductor Package Maintainer	An R packaged zlib-1.2.5

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