Bioconductor Software Packages

Bioconductor version: 3.7

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
adaptest	Weixin Cai	Data-Adaptive Statistics for High-Dimensional Multiple Testing
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	Ben Bolstad	Tools for parsing Affymetrix data files
affylmGUI	Gordon Smyth	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
amplican	Eivind Valen	Automated analysis of CRISPR experiments
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
ANF	Tianle Ma	Affinity Network Fusion for Complex Patient Clustering
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
AnnotationFilter	Bioconductor Maintainer	Facilities for Filtering Bioconductor Annotation Resources
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).
anota2seq	Christian Oertlin, Julie Lorent	Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
antiProfiles	Hector Corrada Bravo	Implementation of gene expression anti-profiles
apComplex	Denise Scholtens	Estimate protein complex membership using AP-MS protein data
apeglm	Anqi Zhu	Approximate posterior estimation for GLM coefficients
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	Mike Smith	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
ASICS	Gaëlle Lefort	Automatic Statistical Identification in Complex Spectra
ASpli	Estefania Mancini	Analysis of alternative splicing using RNA-Seq
ASSET	Samsiddhi Bhattacharjee	An R package for subset-based association analysis of heterogeneous traits and subtypes
ASSIGN	Ying Shen, W. Evan Johnson, David Jenkins, Mumtehena Rahman	Adaptive Signature Selection and InteGratioN (ASSIGN)
ATACseqQC	Jianhong Ou	ATAC-seq Quality Control
attract	Samuel Zimmerman	Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
AUCell	Sara Aibar	AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
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
banocc	Emma Schwager	Bayesian ANalysis Of Compositional Covariance
basecallQC	Thomas Carroll	Working with Illumina Basecalling and Demultiplexing input and output files
BaseSpaceR	Jared O'Connell	R SDK for BaseSpace RESTful API
Basic4Cseq	Carolin Walter	Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
BASiCS	Catalina A. Vallejos, Nils Eling	Bayesian Analysis of Single-Cell Sequencing 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
bcSeq	Jiaxing Lin	Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens
beachmat	Aaron Lun	Compiling Bioconductor to Handle Each Matrix Type
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
BEARscc	Benjamin Schuster-Boeckler	BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)
BEAT	Kemal Akman	BEAT - BS-Seq Epimutation Analysis Toolkit
BEclear	David Rasp	Correct for batch effects in DNA methylation data
bgafun	Iain Wallace	BGAfun A method to identify specifity determining residues in protein families
BgeeDB	Julien Wollbrett, Julien Roux, 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
BiFET	Ahrim Youn	Bias-free Footprint Enrichment Test
BiGGR	Anand K. Gavai, Hannes Hettling	Constraint based modeling in R using metabolic reconstruction databases
bigmelon	Tyler J. 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
BiocFileCache	Lori Shepherd	Manage Files Across Sessions
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
BiocOncoTK	VJ Carey	Bioconductor components for general cancer genomics
BioCor	Lluís Revilla Sancho	Functional similarities
BiocParallel	Bioconductor Package Maintainer	Bioconductor facilities for parallel evaluation
BiocSklearn	VJ Carey	interface to python sklearn via Rstudio reticulate
BiocStyle	Bioconductor Package Maintainer	Standard styles for vignettes and other Bioconductor documents
BiocVersion	Bioconductor Package Maintainer	Set the appropriate version of Bioconductor packages
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	Mike Smith	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
BioNetStat	Vinicius Jardim	Biological Network Analysis
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	Efficient manipulation of biological strings
biosvd	Anneleen Daemen, Matthew Brauer	Package for high-throughput data processing, outlier detection, noise removal and dynamic modeling
biotmle	Nima Hejazi	Moderated and Targeted Statistical Learning for Biomarker Discovery
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	Vojtěch Kulvait	Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level
BLMA	Tin Nguyen	BLMA: A package for bi-level meta-analysis
bnbc	Kipper Fletez-Brant	Bandwise normalization and batch correction of Hi-C data
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*)
branchpointer	Beth Signal	Prediction of intronic splicing branchpoints
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	Software infrastructure for efficient representation of full genomes and their SNPs
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	Ben Bolstad	A matrix data storage object held in temporary files
BufferedMatrixMethods	Ben Bolstad	Microarray Data related methods that utlize BufferedMatrix objects
BUMHMM	Alina Selega	Computational pipeline for computing probability of modification from structure probing experiment data
bumphunter	Rafael A. Irizarry	Bump Hunter
BUS	Yuanhua Liu	Gene network reconstruction
CAFE	Sander Bollen	Chromosmal Aberrations Finder in Expression data
CAGEfightR	Malte Thodberg	Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
CAGEr	Vanja Haberle, Charles Plessy	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 multiple genomic data sets
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
CATALYST	Helena L. Crowell	Cytometry dATa anALYSis Tools
Category	Bioconductor Package Maintainer	Category Analysis
categoryCompare	Robert M. Flight	Meta-analysis of high-throughput experiments using feature annotations
CausalR	Glyn Bradley, Steven Barrett	Causal network analysis methods
cbaf	Arman Shahrisa	Multiple automated functions for cbioportal.org
ccfindR	Jun Woo	Cancer Clone Finder
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
cellbaseR	Mohammed OE Abdallah	Querying annotation data from the high performance Cellbase web
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	A.Gabor	Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
cellscape	Maia Smith	Explores single cell copy number profiles in the context of a single cell tree
CellScore	Nancy Mah	Tool for Evaluation of Cell Identity from Transcription Profiles
cellTree	David duVerle	Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
CEMiTool	Helder Nakaya	Co-expression Modules identification Tool
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
CHARGE	Benjamin Mayne	CHARGE: CHromosome Assessment in R from Gene Expression data
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
ChIC	Carmen Maria Livi	Quality Control Pipeline for ChIP-Seq Data
Chicago	Mikhail Spivakov	CHiCAGO: Capture Hi-C Analysis of Genomic Organization
chimera	Raffaele A Calogero	A package for secondary analysis of fusion products
chimeraviz	Stian Lågstad	Visualization tools for gene fusions
ChIPanalyser	Patrick C.N. Martin	ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPComp	Li Chen	Quantitative comparison of multiple ChIP-seq datasets
chipenrich	Raymond G. Cavalcante	Gene Set Enrichment For ChIP-seq Peak Data
ChIPexoQual	Rene Welch	ChIPexoQual
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
ChIPSeqSpike	Nicolas Descostes	ChIP-Seq data scaling according to spike-in control
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	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
chromswitch	Selin Jessa	An R package to detect chromatin state switches from epigenomic data
chromVAR	Alicia Schep	Chromatin Variation Across Regions
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 cross-validated 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
ClusterJudge	Adrian Pasculescu	Judging Quality of Clustering Methods using Mutual Information
clusterProfiler	Guangchuang Yu	statistical analysis and visualization of functional profiles for genes and gene clusters
clusterSeq	Thomas J. Hardcastle	Clustering of high-throughput sequencing data by identifying co-expression patterns
ClusterSignificance	Jason T Serviss	The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from 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
coexnet	Juan David Henao	coexnet: An R package to build CO-EXpression NETworks from Microarray Data
CoGAPS	Elana J. Fertig, Thomas D. Sherman	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
consensusOV	Benjamin Haibe-Kains	Gene expression-based subtype classification for high-grade serous ovarian cancer
consensusSeekeR	Astrid 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
CORREP	Dongxiao Zhu	Multivariate Correlation Estimator and Statistical Inference Procedures.
coseq	Andrea Rau	Co-Expression Analysis of Sequencing Data
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.
CTDquerier	Carles Hernandez-Ferrer	Package for CTDbase data query, visualization and downstream analysis
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 Bo Wen	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
cydar	Aaron Lun	Using Mass Cytometry for Differential Abundance Analyses
CytoDx	Zicheng Hu	Robust prediction of clinical outcomes using cytometry data without cell gating
cytofkit	Jinmiao Chen, Matthew Myint	cytofkit: an integrated mass cytometry data analysis pipeline
cytolib	Mike Jiang	C++ infrastructure for representing and interacting with the gated cytometry
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
DaMiRseq	Mattia Chiesa	Data Mining for RNA-seq data: normalization, feature selection and classification
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)
ddPCRclust	Benedikt G. Brink	Clustering algorithm for ddPCR data
debrowser	Alper Kucukural	Interactive Differential Expresion Analysis Browser
DECIPHER	Erik Wright	Tools for curating, analyzing, and manipulating biological sequences
DEComplexDisease	Guofeng Meng	A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis
DeconRNASeq	Ting Gong	Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
decontam	Benjamin Callahan	Identify Contaminants in Marker-gene and Metagenomics Sequencing 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
DelayedArray	Hervé Pagès	Delayed operations on array-like objects
DelayedMatrixStats	Peter Hickey	Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
deltaGseg	Diana Low	deltaGseg
DeMAND	Jung Hoon Woo, Mariano Alvarez	DeMAND
DEP	Arne Smits	Differential Enrichment analysis of Proteomics data
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
DEScan2	Dario Righelli	Differential Enrichment Scan 2
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
DEsingle	Zhun Miao	DEsingle for detecting three types of differential expression in single-cell RNA-seq data
destiny	Philipp Angerer	Creates diffusion maps
DEsubs	Aristidis G. Vrahatis, 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
diffcoexp	Wenbin Wei	Differential Co-expression Analysis
diffcyt	Lukas M. Weber	Differential discovery in high-dimensional cytometry via high-resolution clustering
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 biooligomer motifs
diffloop	Caleb Lareau	Identifying differential DNA loops from chromatin topology data
diffuStats	Sergio Picart-Armada	Diffusion scores on biological networks
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
discordant	Charlotte Siska	The Discordant Method: A Novel Approach for Differential Correlation
dks	Jeffrey T. Leek	The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.
DMCHMM	Farhad Shokoohi	Differentially Methylated CpG using Hidden Markov Model
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
DMRScan	Christian M Page	Detection of Differentially Methylated Regions
dmrseq	Keegan Korthauer	Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
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
DominoEffect	Marija Buljan, Peter Blattmann	Identification and Annotation of Protein Hotspot Residues
doppelgangR	Levi Waldron	Identify likely duplicate samples from genomic or meta-data
DOQTL	Daniel Gatti	Genotyping and QTL Mapping in DO Mice
Doscheda	Bruno Contrino	A DownStream Chemo-Proteomics Analysis Pipeline
DOSE	Guangchuang Yu	Disease Ontology Semantic and Enrichment analysis
drawProteins	Paul Brennan	Package to Draw Protein Schematics from Uniprot API output
DRIMSeq	Malgorzata Nowicka	Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
DriverNet	Jiarui Ding	Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer
DropletUtils	Aaron Lun	Utilities for Handling Single-Cell Droplet Data
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 shrinkage 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	Tiago Chedraoui Silva	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
enrichplot	Guangchuang Yu	Visualization of Functional Enrichment Result
ensembldb	Johannes Rainer	Utilities to create and use Ensembl-based annotation databases
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
EpiDISH	Shijie Charles Zheng	Epigenetic Dissection of Intra-Sample-Heterogeneity
epigenomix	Hans-Ulrich Klein	Epigenetic and gene transcription data normalization and integration with mixture models
epiNEM	Martin Pirkl	epiNEM
epivizr	Hector Corrada Bravo	R Interface to epiviz web app
epivizrChart	Hector Corrada Bravo	R interface to epiviz web components
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
esATAC	Zheng Wei, Wei Zhang	An Easy-to-use Systematic pipeline for ATACseq data analysis
esetVis	Laure Cougnaud	Visualizations of expressionSet Bioconductor object
eudysbiome	Xiaoyuan Zhou	Cartesian plot and contingency test on 16S Microbial data
EventPointer	Juan Pablo Romero	An effective identification of alternative splicing events using junction arrays and RNA-Seq data
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)
FELLA	Sergio Picart-Armada	Interpretation and enrichment for metabolomics data
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
flowTime	R. Clay Wright	Annotation and analysis of biological dynamical systems using flow cytometry
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
funtooNorm	Kathleen Klein	Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
GA4GHclient	Welliton Souza	A Bioconductor package for accessing GA4GH API data servers
GA4GHshiny	Welliton Souza	Shiny application for interacting with GA4GH-based data servers
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
GARS	Mattia Chiesa	GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets
GateFinder	Nima Aghaeepour	Projection-based Gating Strategy Optimization for Flow and Mass Cytometry
gaucho	Alex Murison, Christopher Wardell	Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering
gcapc	Mingxiang Teng	GC Aware Peak Caller
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	Peter Haverty	Suite of Functions for Pooled Crispr Screen QC and Analysis
gcrma	Z. Wu	Background Adjustment Using Sequence Information
GDCRNATools	Ruidong Li, Han Qu	GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
GDSArray	Qian Liu	Representing GDS files as array-like objects
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
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
geneClassifiers	R Kuiper	Application of gene classifiers
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 of orthologous groups
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	Stephanie M. Gogarten, 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
GeneStructureTools	Beth Signal	Tools for spliced gene structure manipulation and analysis
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	Optimized Functional Annotation Of ChIP-seq Data
GENIE3	Van Anh Huynh-Thu	GEne Network Inference with Ensemble of trees
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, Katarzyna Wreczycka	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
GenomicDataCommons	Sean Davis	NIH / NCI Genomic Data Commons Access
GenomicFeatures	Bioconductor Package Maintainer	Tools for making and manipulating transcript centric annotations
GenomicFiles	Bioconductor Package Maintainer	Distributed computing by file or by range
GenomicInteractions	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
GenomicScores	Robert Castelo	Infrastructure to work with genomewide position-specific scores
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 Bayesian inference and statistical learning techniques
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)
GEOsubmission	Alexandre Kuhn	Prepares microarray data for submission to GEO
gep2pep	Francesco Napolitano	Creation and Analysis of Pathway Expression Profiles (PEPs)
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
GISPA	Bhakti Dwivedi	GISPA: Method for Gene Integrated Set Profile Analysis
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
GOfuncR	Steffi Grote	Gene ontology enrichment using FUNC
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
goSTAG	Brian D. Bennett	A tool to use GO Subtrees to Tag and Annotate Genes within a set
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, Mario Medvedovic	Calculate growth-rate inhibition (GR) metrics
groHMM	Anusha Nagari, Tulip Nandu, W. Lee Kraus	GRO-seq Analysis Pipeline
GRridge	Mark A. van de Wiel	Better prediction by use of co-data: Adaptive group-regularized ridge regression
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
GSEABenchmarkeR	Ludwig Geistlinger	Reproducible GSEA Benchmarking
GSEAlm	Assaf Oron	Linear Model Toolset for Gene Set Enrichment Analysis
gsean	Dongmin Jung	Gene Set Enrichment Analysis with Networks
GSReg	Bahman Afsari, Elana J. Fertig	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	Robert Ivanek	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
HDF5Array	Hervé Pagès	HDF5 back end for DelayedArray objects
HDTD	Anestis Touloumis	Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
heatmaps	Malcolm Perry	Flexible Heatmaps for Functional Genomics and Sequence Features
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
HiCcompare	John Stansfield	HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
hicrep	Tao Yang	Measuring the reproducibility of Hi-C data
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
hipathia	Marta R. Hidalgo	HiPathia: High-throughput Pathway Analysis
hiReadsProcessor	Nirav V Malani	Functions to process LM-PCR reads from 454/Illumina data
HiTC	Nicolas Servant	High Throughput Chromosome Conformation Capture analysis
hmdbQuery	VJ Carey	utilities for exploration of human metabolome database
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
iCNV	Zilu Zhou	Integrated Copy Number Variation detection
iCOBRA	Charlotte Soneson	Comparison and Visualization of Ranking and Assignment Methods
ideal	Federico Marini	Interactive Differential Expression AnaLysis
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
igvR	Paul Shannon	igvR: integrative genomics viewer
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
IMAS	Seonggyun Han	Integrative analysis of Multi-omics data for Alternative Splicing
Imetagene	Audrey Lemacon	A graphical interface for the metagene package
IMMAN	Minoo Ashtiani	Interlog protein network reconstruction by Mapping and Mining ANalysis
ImmuneSpaceR	ImmuneSpace Package Maintainer	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
ImpulseDE2	David S Fischer	Differential expression analysis of longitudinal count data sets
impute	Balasubramanian Narasimhan	impute: Imputation for microarray data
InPAS	Jianhong Ou, Lihua Julie Zhu	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
InTAD	Konstantin Okonechnikov	Search for correlation between epigenetic signals and gene expression in TADs
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
IntEREst	Ali Oghabian, Mikko Frilander	Intron-Exon Retention Estimator
InterMineR	InterMine Team	R Interface with InterMine-Powered Databases
IntramiRExploreR	Surajit Bhattacharya	Predicting Targets for Drosophila Intragenic miRNAs
inveRsion	Alejandro Caceres	Inversions in genotype data
IONiseR	Mike Smith	Quality Assessment Tools for Oxford Nanopore MinION data
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
IrisSpatialFeatures	Daniel Gusenleitner	A package to extract spatial features based on multiplex IF images
iSEE	Federico Marini	Interactive SummarizedExperiment Explorer
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
IsoformSwitchAnalyzeR	Kristoffer Vitting-Seerup	An R package to Identify, Annotate and Visualize Isoform Switches with Functional Consequences (from RNA-seq 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
iterClust	Hongxu Ding	Iterative Clustering
iteremoval	Jiacheng Chuan	Iteration removal method for feature selection
IVAS	Seonggyun Han	Identification of genetic Variants affecting Alternative Splicing
ivygapSE	VJ Carey	A SummarizedExperiment for Ivy-GAP data
IWTomics	Marzia A Cremona	Interval-Wise Testing for Omics Data
JASPAR2018	Ge Tan	Data package for JASPAR 2018
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
karyoploteR	Bernat Gel	Plot customizable linear genomes displaying arbitrary 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, Mario Medvedovic	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
kissDE	Aurélie Siberchicot	Retrieves Condition-Specific Variants in RNA-Seq 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, Olivier Francois	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	Gordon Smyth	GUI for limma Package With Two Color Microarrays
LINC	Manuel Goepferich	co-expression of lincRNAs and protein-coding genes
LineagePulse	David S Fischer	Differential expression analysis and model fitting for single-cell RNA-seq data
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
loci2path	Tianlei Xu	Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
logicFS	Holger Schwender	Identification of SNP Interactions
logitT	Tobias Guennel	logit-t Package
Logolas	Kushal Dey	EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices
lol	Yinyin Yuan	Lots Of Lasso
LOLA	Nathan Sheffield	Locus 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
M3C	Christopher John	Monte Carlo Consensus Clustering
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
MACPET	Ioannis Vardaxis	Model based analysis for paired-end 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
MAGeCKFlute	Wubing Zhang	Integrative analysis pipeline for pooled CRISPR functional genetic screens
maigesPack	Gustavo H. Esteves	Functions to handle cDNA microarray data, including several methods of data analysis
MAIT	Pol Sola-Santos	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
mapscape	Maia Smith	mapscape
marray	Yee Hwa (Jean) Yang	Exploratory analysis for two-color spotted microarray data
martini	Hector Climente-Gonzalez	GWAS Incorporating Networks
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
MaxContrastProjection	Jan Sauer	Perform a maximum contrast projection of 3D images along the z-dimension into 2D
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
MCbiclust	Robert Bentham	Massive correlating biclusters for gene expression data and associated methods
MCRestimate	Marc Johannes	Misclassification error estimation with cross-validation
mCSEA	Jordi Martorell-Marugán	Methylated CpGs Set Enrichment Analysis
mdgsa	David Montaner	Multi Dimensional Gene Set Analysis.
mdp	Helder Nakaya	Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
mdqc	Gabriela Cohen-Freue	Mahalanobis Distance Quality Control for microarrays
MDTS	Jack M.. Fu	Detection of de novo deletion in targeted sequencing trios
MEAL	Carlos Ruiz-Arenas	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
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
MetaCyto	Zicheng Hu	MetaCyto: A package for meta-analysis of cytometry data
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
MetaGxOvarian	Michael Zon	Transcriptomic Ovarian Cancer Datasets
metahdep	John R. Stevens	Hierarchical Dependence in Meta-Analysis
metaMS	Ron Wehrens	MS-based metabolomics annotation pipeline
MetaNeighbor	Manthan Shah	Single cell replicability analysis
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.
metavizr	Hector Corrada Bravo	R Interface to the metaviz web app for interactive metagenomics data analysis and visualization
MetCirc	Thomas Naake	Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
methimpute	Aaron Taudt	Imputation-guided re-construction of complete methylomes from WGBS data
methInheritSim	Pascal Belleau	Simulating Whole-Genome Inherited Bisulphite Sequencing 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
methylInheritance	Astrid Deschenes	Permutation-Based Analysis associating Conserved Differentially Methylated Elements from One Generation to the Next to a Treatment Effect
methylKit	Altuna Akalin, Alexander Gosdschan	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
methyvim	Nima Hejazi	Targeted Variable Importance for Differential Methylation Analysis
mfa	Kieran Campbell	Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations
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
microbiome	Leo Lahti	Microbiome Analytics
microRNA	"James F. Reid"	Data and functions for dealing with microRNAs
MIGSA	Juan C. Rodriguez	Massive and Integrative Gene Set Analysis
mimager	Aaron Wolen	mimager: The Microarray Imager
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
MIRA	John Lawson	Methylation-Based Inference of Regulatory Activity
MiRaGE	Y-h. Taguchi	MiRNA Ranking by Gene Expression
miRBaseConverter	Taosheng Xu	A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions
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
miRmine	Dusan Randjelovic	Data package with miRNA-seq datasets from miRmine database as RangedSummarizedExperiment
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
miRsponge	Junpeng Zhang	Identification and analysis of miRNA sponge interaction networks and modules
Mirsynergy	Yue Li	Mirsynergy
missMethyl	Belinda Phipson, Jovana Maksimovic, Andrew Lonsdale	Analysing Illumina HumanMethylation BeadChip Data
missRows	Gonzalez Ignacio	Handling Missing Individuals in Multi-Omics Data Integration
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
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
motifcounter	Wolfgang Kopp	R package for analysing TFBSs in DNA sequences
MotifDb	Paul Shannon	An Annotated Collection of Protein-DNA Binding Sequence Motifs
motifmatchr	Alicia Schep	Fast Motif Matching in R
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
mpra	Leslie Myint	Analyze massively parallel reporter assays
mQTL.NMR	Lyamine Hedjazi	Metabolomic Quantitative Trait Locus Mapping for 1H NMR data
msa	Ulrich Bodenhofer	Multiple Sequence Alignment
msgbsR	Benjamin Mayne	msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions
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 Mass Spectrometry and 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
MSstatsQC	Eralp Dogu	Longitudinal system suitability monitoring and quality control for proteomic experiments
MSstatsQCgui	Eralp Dogu	A graphical user interface for MSstatsQC package
Mulcom	Claudio Isella	Calculates Mulcom test
MultiAssayExperiment	Marcel Ramos	Software for the integration of multi-omics experiments in Bioconductor
multiClust	Nathan Lawlor	multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
MultiDataSet	Carlos Ruiz-Arenas	Implementation of MultiDataSet and ResultSet
MultiMed	Simina M. Boca	Testing multiple biological mediators simultaneously
multiMiR	Matt Mulvahill	Integration of multiple microRNA-target databases with their disease and drug associations
multiOmicsViz	Jing Wang	Plot the effect of one omics data on other omics data along the chromosome
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	Comprehensive genome-wide analysis of mutational processes
MVCClass	Elizabeth Whalen	Model-View-Controller (MVC) Classes
MWASTools	Andrea Rodriguez-Martinez, Rafael Ayala	MWASTools: an integrated pipeline to perform metabolome-wide association studies
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	Steffen Neumann, Laurent Gatto, Qiang Kou	parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
NADfinder	Jianhong Ou, Lihua Julie Zhu	Call wide peaks for sequencing data
NanoStringDiff	tingting zhai,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
ndexr	Florian Auer	NDEx R client library
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
netReg	Simon Dirmeier	Network-Regularized Regression Models
netresponse	Leo Lahti	Functional Network Analysis
NetSAM	Bing Zhang	Network Seriation And Modularization
netSmooth	Jonathan Ronen	Network smoothing for scRNAseq
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
OmaDB	Klara Kaleb, Adrian Altenhoff	R wrapper for the OMA REST API
omicade4	Chen Meng	Multiple co-inertia analysis of omics datasets
OmicCircos	Ying Hu	High-quality circular visualization of omics data
omicplotR	Daniel Giguere	Visual Exploration of Omic Datasets Using a Shiny App
omicRexposome	Carles Hernandez-Ferrer	Exposome and omic data associatin and integration analysis
OmicsMarkeR	Charles E. Determan Jr.	Classification and Feature Selection for 'Omics' Datasets
omicsPrint	Davy Cats	Cross omic genetic fingerprinting
Onassis	Eugenia Galeota	OnASSIs Ontology Annotation and Semantic SImilarity software
oncomix	Daniel Pique	Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data
OncoScore	Daniele Ramazzotti	A tool to identify potentially oncogenic genes
OncoSimulR	Ramon Diaz-Uriarte	Forward Genetic Simulation of Cancer Progression with Epistasis
oneSENSE	Yong Kee Tan	One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)
ontoProc	VJ Carey	processing of ontologies of anatomy, cell lines, and so on
openCyto	Mike Jiang	Hierarchical Gating Pipeline for flow cytometry data
openPrimeR	Matthias Döring	Multiplex PCR Primer Design and Analysis
openPrimeRui	Matthias Döring	Shiny Application for Multiplex PCR Primer Design and Analysis
oposSOM	Henry Loeffler-Wirth	Comprehensive analysis of transciptome data
oppar	Soroor Hediyeh zadeh	Outlier profile and pathway analysis in R
OPWeight	Mohamad Hasan	Optimal p-value weighting with independent information
OrderedList	Claudio Lottaz	Similarities of Ordered Gene Lists
ORFik	Kornel Labun	Open Reading Frames in Genomics
Organism.dplyr	Martin Morgan	dplyr-based Access to Bioconductor Annotation Resources
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
panelcn.mops	Gundula Povysil	CNV detection tool for targeted NGS panel data
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, Yue Zhao	PathoStat Statistical Microbiome Analysis Package
pathprint	Sokratis Kariotis	Pathway fingerprinting for analysis of gene expression arrays
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
PathwaySplice	Aimin Yan	An R Package for Unbiased Splicing Pathway Analysis
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
pcxn	Sokratis Kariotis	Exploring, analyzing and visualizing functions utilizing the pcxnData package
pdInfoBuilder	Benilton Carvalho	Platform Design Information Package Builder
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.
perturbatr	Simon Dirmeier	Statistical Analysis of High-Throughput Genetic Perturbation Screens
PGA	Bo Wen, Shaohang Xu	An package for identification of novel peptides by customized database derived from RNA-Seq
pgca	Gabriela Cohen-Freue	PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data
PGSEA	Karl Dykema	Parametric Gene Set Enrichment Analysis
phantasus	Alexey Sergushichev	Visual and interactive gene expression analysis
PharmacoGx	Benjamin Haibe-Kains	Analysis of Large-Scale Pharmacogenomic Data
phenoDist	Xian Zhang	Phenotypic distance measures
phenopath	Kieran Campbell	Genomic trajectories with heterogeneous genetic and environmental backgrounds
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	Hamed Haselimashhadi	Statistical analysis of phenotypic data
philr	Justin Silverman	Phylogenetic partitioning based ILR transform for metagenomics data
phosphonormalizer	Sohrab Saraei	Compensates for the bias introduced by median normalization in phosphoproteomics
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 and Pathway 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	Bioconductor Core Team	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.
plyranges	Stuart Lee	A fluent interface for manipulating GenomicRanges
pmm	Anna Drewek	Parallel Mixed Model
podkat	Ulrich Bodenhofer	Position-Dependent Kernel Association Test
pogos	VJ Carey	PharmacOGenomics Ontology Support
polyester	Jack Fu, Jeff Leek	Simulate RNA-seq reads
Polyfit	Conrad Burden	Add-on to DESeq to improve p-values and q-values
POST	Xueyuan Cao	Projection onto Orthogonal Space Testing for High Dimensional Data
PowerExplorer	Xu Qiao	Power Estimation Tool for RNA-Seq and proteomics data
powerTCR	Hillary Koch	Model-Based Comparative Analysis of the TCR Repertoire
PPInfer	Dongmin Jung	Inferring functionally related proteins using protein interaction networks
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 Analysis
predictionet	Benjamin Haibe-Kains, Catharina Olsen	Inference for predictive networks designed for (but not limited to) genomic data
preprocessCore	Ben 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
progeny	Michael Schubert	Pathway RespOnsive GENes for activity inference from gene expression
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
PROPS	Lichy Han	PRObabilistic Pathway Score (PROPS)
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	Maren Sitte	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
RaggedExperiment	Martin Morgan	Representation of Sparse Experiments and Assays Across Samples
rain	Paul F. Thaben	Rhythmicity Analysis Incorporating Non-parametric Methods
rama	Raphael Gottardo	Robust Analysis of MicroArrays
RamiGO	Markus Schroeder	AmiGO visualize R interface
ramwas	Andrey A Shabalin	Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
RandomWalkRestartMH	Alberto Valdeolivas Urbelz	Random walk with restart on multiplex and heterogeneous Networks
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	A suite for analysis of rare genomic 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
Rbowtie2	Zheng Wei	An R Wrapper for Bowtie2 and AdapterRemoval
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, Fathi Elloumi	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
RcisTarget	Sara Aibar	RcisTarget: Identify transcription factor binding motifs enriched on a gene list
Rcpi	Nan Xiao	Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
RCy3	Alexander Pico, Tanja Muetze, Paul Shannon	Functions to Access and Control Cytoscape
RCyjs	Paul Shannon	Display and manipulate graphs in cytoscape.js
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	L1-regularization based methods for detection of differential splicing
REMP	Yinan Zheng	Repetitive Element Methylation Prediction
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
restfulSE	Shweta Gopaulakrishnan	Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
rexposome	Carles Hernandez-Ferrer	Exposome exploration and outcome data analysis
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
Rgin	Hector Climente	gin in R
RGMQL	Simone Pallotta	GenoMetric Query Language for R/Bioconductor
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	Mike Smith	HDF5 interface to R
rhdf5client	Samuela Pollack	Access HDF5 content from h5serv
Rhdf5lib	Mike Smith	hdf5 library as an R package
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	Zicheng Hu, 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
RITAN	Michael Zimmermann	Rapid Integration of Term Annotation and Network resources
RIVER	Yungil Kim	R package for RIVER (RNA-Informed Variant Effect on Regulation)
RJMCMCNucleosomes	Astrid Deschênes	Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
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
RNAdecay	Reed Sorenson	Maximum Likelihood Decay Modeling of RNA Degradation Data
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
RProtoBufLib	Mike Jiang	C++ headers and static libraries of Protocol buffers
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
rqt	Ilya Y. Zhbannikov	rqt: utilities for gene-level meta-analysis
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
RSeqAn	August Guang	R SeqAn
rSFFreader	Matt Settles	rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers
Rsubread	Wei Shi, Yang Liao and Gordon K Smyth	Subread sequence alignment and counting 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	Marcel Ramos	A new tool for exporting TCGA Firehose data
RTN	Mauro Castro	Reconstruction of transcriptional networks and analysis of master regulators
RTNduals	Mauro Castro, Clarice Groeneveld	Analysis of co-regulation and inference of 'dual regulons'
RTNsurvival	Clarice Groeneveld, Mauro A. A. Castro	Survival analysis using transcriptional networks inferred by the RTN package
RTopper	Luigi Marchionni	This package is designed to perform Gene Set Analysis across multiple genomic platforms
rtracklayer	Michael Lawrence	R interface to genome annotation files and the UCSC genome browser
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
runibic	Patryk Orzechowski	runibic: row-based biclustering algorithm for analysis of gene expression data in R
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
RVS	Thomas Sherman	Computes estimates of the probability of related individuals sharing a rare variant
rWikiPathways	Egon Willighagen, Alexander Pico	rWikiPathways - R client library for the WikiPathways API
S4Vectors	Bioconductor Package Maintainer	S4 implementation of vector-like and list-like objects
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
samExploreR	shailesh tripathi	samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
sampleClassifier	Khadija El Amrani	Sample Classifier
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
Scale4C	Carolin Walter	Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
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
scDD	Keegan Korthauer	Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
scde	Jean Fan	Single Cell Differential Expression
scFeatureFilter	Guillaume Devailly	A correlation-based method for quality filtering of single-cell RNAseq data
scfind	Vladimir Kiselev	A search tool for single cell RNA-seq data by gene lists
ScISI	Tony Chiang	In Silico Interactome
scmap	Vladimir Kiselev	A tool for unsupervised projection of single cell RNA-seq data
scmeth	Divy Kangeyan	Functions to conduct quality control analysis in methylation data
SCnorm	Rhonda Bacher	Normalization of single cell RNA-seq data
scone	Michael Cole	Single Cell Overview of Normalized Expression data
Sconify	Tyler J Burns	A toolkit for performing KNN-based statistics for flow and mass cytometry data
scoreInvHap	Carlos Ruiz	Get inversion status in predefined regions
scPipe	Luyi Tian	pipeline for single cell RNA-seq data analysis
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
SDAMS	Yuntong Li	Differential Abundant Analysis for Metabolomics and Proteomics Data
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
semisup	Armin Rauschenberger	Detecting SNPs with interactive effects on a quantitative trait
SEPA	Zhicheng Ji	SEPA
SEPIRA	Yuting Chen	Systems EPigenomics Inference of Regulatory Activity
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
seqCAT	Erik Fasterius	High Throughput Sequencing Cell Authentication Toolkit
seqCNA	David Mosen-Ansorena	Copy number analysis of high-throughput sequencing cancer data
seqcombo	Guangchuang Yu	Visualization Tool for Sequence Recombination and Reassortment
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
seqsetvis	Joseph R Boyd	Set Based Visualizations for Next-Gen Sequencing Data
SeqSQC	Qian Liu	A bioconductor package for sample quality check with next generation sequencing data
seqTools	Wolfgang Kaisers	Analysis of nucleotide, sequence and quality content on fastq files
SeqVarTools	Stephanie M. Gogarten	Tools for variant data
sevenbridges	Nan Xiao	Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
sevenC	Jonas Ibn-Salem	Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
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
SIAMCAT	Konrad Zych	Statistical Inference of Associations between Microbial Communities And host phenoTypes
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
signet	Alexandre Gouy	signet: Selection Inference in Gene NETworks
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	M. R. Nezami Ranjbar	GC-SIM-MS data processing and alaysis tool
SimBindProfiles	Bettina Fischer	Similar Binding Profiles
similaRpeak	Astrid Deschenes	Metrics to estimate a level of similarity between two ChIP-Seq profiles
SIMLR	Daniele Ramazzotti	Title: SIMLR and CIMLR Multi-kernel LeaRning methods
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
SingleCellExperiment	Davide Risso	S4 Classes for Single Cell Data
singleCellTK	David Jenkins	Interactive Analysis of Single Cell RNA-Seq Data
singscore	Ruqian Lyu	Rank-based single-sample gene set scoring method
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
slalom	Davis McCarthy	Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
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.
sparseDOSSA	Boyu Ren, Emma Schwager, George Weingart	Sparse Data Observations for Simulating Synthetic Abundance
SparseSignatures	Luca De Sano	SparseSignatures
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
splatter	Luke Zappia	Simple Simulation of Single-cell RNA Sequencing Data
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
SPONGE	Markus List	Sparse Partial Correlations On Gene Expression
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 to gene mutations from transcriptomics data from transcriptomics data
srnadiff	Matthias Zytnicki	Differential Expression of Small RNA-Seq
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
stageR	Koen Van den Berge	stageR: stage-wise analysis of high throughput gene expression data in R
STAN	Rafael Campos-Martin	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, Núria Planell	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
Streamer	Martin Morgan	Enabling stream processing of large files
STRINGdb	Damian Szklarczyk	STRINGdb (Search Tool for the Retrieval of Interacting proteins database)
STROMA4	Sadiq Saleh	Assign Properties to TNBC Patients
subSeq	Andrew J. Bass, John D. Storey	Subsampling of high-throughput sequencing count data
SummarizedBenchmark	Alejandro Reyes, Patrick Kimes	Classes and methods for performing benchmark comparisons
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 estimate the hidden factors of unwanted variability and adjust for them to enable a more powerful and accurate differential expression analysis 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 statistical data analysis
swfdr	Simina M. Boca, Jeffrey T. Leek	Science-wise false discovery rate and proportion of true null hypotheses estimation
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 GDC data
TCGAbiolinksGUI	Tiago C. Silva	"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
TCGAutils	Marcel Ramos	TCGA utility functions for data management
TCseq	Mengjun Wu	Time course sequencing data analysis
TDARACNE	Zoppoli Pietro	Network reverse engineering from time course data.
tenXplore	VJ Carey	ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics
TEQC	Manuela Hummel	Quality control for target capture experiments
ternarynet	Matthew N. McCall	Ternary Network Estimation
TFARM	Liuba Nausicaa Martino	Transcription Factors Association Rules Miner
TFBSTools	Ge Tan	Software Package for Transcription Factor Binding Site (TFBS) Analysis
TFEA.ChIP	Laura Puente Santamaría	Analyze Transcription Factor Enrichment
TFHAZ	Alberto Marchesi	Transcription Factor High Accumulation Zones
TFutils	Shweta Gopaulakrishnan	TFutils
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
timescape	Maia Smith	Patient Clonal Timescapes
TIN	Bjarne Johannessen	Transcriptome instability analysis
TissueEnrich	Ashish Jain	Tissue-specific gene enrichment 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
TMixClust	Monica Golumbeanu	Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines
TnT	Jialin Ma	Interactive Visualization for Genomic Features
tofsims	Lorenz Gerber	Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
ToPASeq	Ludwig Geistlinger	Topology-based pathway analysis of RNA-seq data
topdownr	Sebastian Gibb	Investigation of Fragmentation Conditions in Top-Down Proteomics
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 R/Bioconductor package for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data
transcriptogramer	Diego Morais	Transcriptional analysis based on transcriptograms
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
treeio	Guangchuang Yu	Base Classes and Functions for Phylogenetic Tree Input and Output
trena	Paul Shannon	Fit transcriptional regulatory networks using gene expression, priors, machine learning
Trendy	Rhonda Bacher	Breakpoint analysis of time-course expression data
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
tRNAscanImport	Felix GM Ernst	Imports a tRNAscan-SE result file as GRanges object
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
TSRchitect	R. Taylor Raborn	Promoter identification from large-scale TSS profiling data
TSSi	Julian Gehring	Transcription Start Site Identification
TTMap	Rachel Jeitziner	Two-Tier Mapper: a clustering tool based on topological data analysis
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
twoddpcr	Anthony Chiu	Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules
tximport	Michael Love	Import and summarize transcript-level estimates for transcript- and gene-level analysis
TxRegInfra	VJ Carey	Metadata management for multiomic specification of transcriptional regulatory networks
TypeInfo	Duncan Temple Lang	Optional Type Specification Prototype
UNDO	Niya Wang	Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions
unifiedWMWqPCR	Joris Meys	Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
UniProt.ws	Marc Carlson	R Interface to UniProt Web Services
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 Exploratory Analysis of Variant Calls
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
vidger	Brandon Monier	Create rapid visualizations of RNAseq data in R
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
vulcan	Federico M. Giorgi	VirtUaL ChIP-Seq data Analysis using 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
wiggleplotr	Kaur Alasoo	Make read coverage plots from BigWig files
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 manipulation 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
zFPKM	Ron Ammar	A suite of functions to facilitate zFPKM transformations
zinbwave	Davide Risso	Zero-Inflated Negative Binomial Model for RNA-Seq Data
zlibbioc	Bioconductor Package Maintainer	An R packaged zlib-1.2.5