Bioconductor Software Packages

Bioconductor version: 3.14

Package	Maintainer	Title
a4	Laure Cougnaud	Automated Affymetrix Array Analysis Umbrella Package
a4Base	Laure Cougnaud	Automated Affymetrix Array Analysis Base Package
a4Classif	Laure Cougnaud	Automated Affymetrix Array Analysis Classification Package
a4Core	Laure Cougnaud	Automated Affymetrix Array Analysis Core Package
a4Preproc	Laure Cougnaud	Automated Affymetrix Array Analysis Preprocessing Package
a4Reporting	Laure Cougnaud	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.
abseqR	JiaHong Fong	Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
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
ACE	Jos B Poell	Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing
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
ADAM	Jose Luiz Rybarczyk Filho	ADAM: Activity and Diversity Analysis Module
ADAMgui	Jose Luiz Rybarczyk Filho	Activity and Diversity Analysis Module Graphical User Interface
adductomicsR	Josie Hayes	Processing of adductomic mass spectral datasets
ADImpute	Ana Carolina Leote	Adaptive Dropout Imputer (ADImpute)
adSplit	Claudio Lottaz	Annotation-Driven Clustering
AffiXcan	Alessandro Lussana	A Functional Approach To Impute Genetically Regulated Expression
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
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
affyPLM	Ben Bolstad	Methods for fitting probe-level models
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
aggregateBioVar	Jason Ratcliff	Differential Gene Expression Analysis for Multi-subject scRNA-seq
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
airpart	Wancen Mu	Differential cell-type-specific allelic imbalance
ALDEx2	Greg Gloor	Analysis Of Differential Abundance Taking Sample Variation Into Account
alevinQC	Charlotte Soneson	Generate QC Reports For Alevin Output
AllelicImbalance	Jesper R Gadin	Investigates Allele Specific Expression
AlphaBeta	Yadollah Shahryary Dizaji	Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
alpine	Michael Love	alpine
ALPS	Venu Thatikonda	AnaLysis routines for ePigenomicS data
AlpsNMR	Sergio Oller Moreno	Automated spectraL Processing System for NMR
alsace	Ron Wehrens	ALS for the Automatic Chemical Exploration of mixtures
altcdfenvs	Laurent Gautier	alternative CDF environments (aka probeset mappings)
AMARETTO	Olivier Gevaert	Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
AMOUNTAIN	Dong Li	Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach
amplican	Eivind Valen	Automated analysis of CRISPR experiments
Anaquin	Ted Wong	Statistical analysis of sequins
ANCOMBC	Huang Lin	Analysis of compositions of microbiomes with bias correction
AneuFinder	Aaron Taudt	Analysis of Copy Number Variation in Single-Cell-Sequencing Data
ANF	Tianle Ma	Affinity Network Fusion for Complex Patient Clustering
animalcules	Yue Zhao	Interactive microbiome analysis toolkit
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	Manipulation of SQLite-based annotations in Bioconductor
AnnotationFilter	Bioconductor Package Maintainer	Facilities for Filtering Bioconductor Annotation Resources
AnnotationForge	Bioconductor Package Maintainer	Tools for building SQLite-based annotation data packages
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
AnVIL	Martin Morgan	Bioconductor on the AnVIL compute environment
AnVILBilling	Vince Carey	Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org).
AnVILPublish	Martin Morgan	Publish Packages and Other Resources to AnVIL Workspaces
APAlyzer	Ruijia Wang	A toolkit for APA analysis using RNA-seq data
apComplex	Denise Scholtens	Estimate protein complex membership using AP-MS protein data
apeglm	Anqi Zhu	Approximate posterior estimation for GLM coefficients
appreci8R	Sarah Sandmann	appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV
aroma.light	Henrik Bengtsson	Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
ArrayExpress	Suhaib Mohammed	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
ARRmNormalization	Jean-Philippe Fortin	Adaptive Robust Regression normalization for Illumina methylation data
artMS	David Jimenez-Morales	Analytical R tools for Mass Spectrometry
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
ASpediaFI	Doyeong Yu	ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
ASpli	Estefania Mancini	Analysis of Alternative Splicing Using RNA-Seq
AssessORF	Deepank Korandla	Assess Gene Predictions Using Proteomics and Evolutionary Conservation
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
atena	Beatriz Calvo-Serra	Analysis of Transposable Elements
atSNP	Sunyoung Shin	Affinity test for identifying regulatory SNPs
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)
autonomics	Aditya Bhagwat	Generifying and intuifying cross-platform omics analysis
Autotuner	Craig McLean	Automated parameter selection for untargeted metabolomics data processing
AWFisher	Zhiguang Huo	An R package for fast computing for adaptively weighted fisher's method
awst	Davide Risso	Asymmetric Within-Sample Transformation
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
bambu	Ying Chen	Reference-guided isoform reconstruction and quantification for long read RNA-Seq data
bamsignals	Johannes Helmuth	Extract read count signals from bam files
BANDITS	Simone Tiberi	BANDITS: Bayesian ANalysis of DIfferenTial Splicing
banocc	George Weingart, Curtis Huttenhower	Bayesian ANalysis Of Compositional Covariance
barcodetrackR	Diego Alexander Espinoza	Functions for Analyzing Cellular Barcoding Data
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	Alan O'Callaghan	Bayesian Analysis of Single-Cell Sequencing data
BasicSTARRseq	Annika Buerger	Basic peak calling on STARR-seq data
basilisk	Aaron Lun	Freezing Python Dependencies Inside Bioconductor Packages
basilisk.utils	Aaron Lun	Basilisk Installation Utilities
batchelor	Aaron Lun	Single-Cell Batch Correction Methods
BatchQC	Solaiappan Manimaran	Batch Effects Quality Control Software
BayesKnockdown	William Chad Young	BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data
BayesSpace	Matt Stone	Clustering and Resolution Enhancement of Spatial Transcriptomes
bayNorm	Wenhao Tang	Single-cell RNA sequencing data normalization
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
BDMMAcorrect	ZHENWEI DAI	Meta-analysis for the metagenomic read counts data from different cohorts
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	Correction of batch effects in DNA methylation data
benchdamic	Matteo Calgaro	Benchmark of differential abundance methods on microbiome data
BgeeCall	Julien Wollbrett	Automatic RNA-Seq present/absent gene expression calls generation
BgeeDB	Julien Wollbrett, Julien Roux, Andrea Komljenovic, Frederic Bastian	Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology
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
bigPint	Lindsay Rutter	Big multivariate data plotted interactively
BindingSiteFinder	Mirko Brüggemann	Binding site defintion based on iCLIP data
bioassayR	Daniela Cassol	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
biobtreeR	Tamer Gur	Using biobtree tool from R
bioCancer	Karim Mezhoud	Interactive Multi-Omics Cancers Data Visualization and Analysis
BiocCheck	Bioconductor Package Maintainer	Bioconductor-specific package checks
BiocDockerManager	Bioconductor Package Maintainer	Access Bioconductor docker images
BiocFileCache	Lori Shepherd	Manage Files Across Sessions
BiocGenerics	Bioconductor Package Maintainer	S4 generic functions used in Bioconductor
biocGraph	Florian Hahne	Graph examples and use cases in Bioinformatics
BiocIO	Bioconductor Package Maintainer	Standard Input and Output for Bioconductor Packages
BiocNeighbors	Aaron Lun	Nearest Neighbor Detection for Bioconductor 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
BiocPkgTools	Sean Davis	Collection of simple tools for learning about Bioc Packages
BiocSet	Kayla Morrell	Representing Different Biological Sets
BiocSingular	Aaron Lun	Singular Value Decomposition for Bioconductor Packages
BiocSklearn	Vince Carey	interface to python sklearn via Rstudio reticulate
BiocStyle	Bioconductor Package	Standard styles for vignettes and other Bioconductor documents
biocthis	Leonardo Collado-Torres	Automate package and project setup for Bioconductor packages
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
biodb	Pierrick Roger	biodb, a library and a development framework for connecting to chemical and biological databases
biodbChebi	Pierrick Roger	biodbChebi, a library for connecting to the ChEBI Database
biodbHmdb	Pierrick Roger	biodbHmdb, a library for connecting to the HMDB Database
biodbKegg	Pierrick Roger	biodbKegg, a library for connecting to the KEGG Database
biodbLipidmaps	Pierrick Roger	biodbLipidmaps, a library for connecting to the Lipidmaps Structure database
biodbUniprot	Pierrick Roger	biodbUniprot, a library for connecting to the Uniprot Database
bioDist	Bioconductor Package Maintainer	Different distance measures
biomaRt	Mike Smith	Interface to BioMart databases (i.e. Ensembl)
biomformat	Paul J. McMurdie	An interface package for the BIOM file format
BioMM	Junfang Chen	BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
BioMVCClass	Elizabeth Whalen	Model-View-Controller (MVC) Classes That Use Biobase
biomvRCNS	Yang Du	Copy Number study and Segmentation for multivariate biological data
BioNERO	Fabricio Almeida-Silva	Biological Network Reconstruction Omnibus
BioNet	Marcus Dittrich	Routines for the functional analysis of biological networks
BioNetStat	Vinicius Jardim	Biological Network Analysis
BioPlex	Ludwig Geistlinger	R-side access to BioPlex protein-protein interaction data
BioQC	Jitao David Zhang	Detect tissue heterogeneity in expression profiles with gene sets
biosigner	Philippe Rinaudo, Etienne Thevenot	Signature discovery from omics data
Biostrings	H. Pagès	Efficient manipulation of biological strings
BioTIP	Yuxi (Jennifer) Sun, Zhezhen Wang, and X Holly Yang	BioTIP: An R package for characterization of Biological Tipping-Point
biotmle	Nima Hejazi	Targeted Learning with Moderated Statistics 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)
biscuiteer	"Jacob Morrison"	Convenience Functions for Biscuit
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
blacksheepr	RugglesLab	Outlier Analysis for pairwise differential comparison
blima	Vojtěch Kulvait	Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level
BLMA	Hung Nguyen	BLMA: A package for bi-level meta-analysis
BloodGen3Module	Darawan Rinchai	This R package for performing module repertoire analyses and generating fingerprint representations
bluster	Aaron Lun	Clustering Algorithms for Bioconductor
bnbc	Kipper Fletez-Brant	Bandwise normalization and batch correction of Hi-C data
bnem	Martin Pirkl	Training of logical models from indirect measurements of perturbation experiments
BPRMeth	Chantriolnt-Andreas Kapourani	Model higher-order methylation profiles
BRAIN	Piotr Dittwald	Baffling Recursive Algorithm for Isotope distributioN calculations
brainflowprobes	Amanda Price	Plots and annotation for choosing BrainFlow target probe sequence
BrainSABER	USD Biomedical Engineering	Brain Span Atlas in Biobase Expressionset R toolset
BrainStars	Itoshi NIKAIDO	query gene expression data and plots from BrainStars (B*)
branchpointer	Beth Signal	Prediction of intronic splicing branchpoints
breakpointR	David Porubsky	Find breakpoints in Strand-seq data
brendaDb	Yi Zhou	The BRENDA Enzyme Database
BRGenomics	Mike DeBerardine	Tools for the Efficient Analysis of High-Resolution Genomics Data
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
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
bugsigdbr	Ludwig Geistlinger	R-side access to published microbial signatures from BugSigDB
BUMHMM	Alina Selega	Computational pipeline for computing probability of modification from structure probing experiment data
bumphunter	Tamilselvi Guharaj	Bump Hunter
BumpyMatrix	Aaron Lun	Bumpy Matrix of Non-Scalar Objects
BUS	Yuanhua Liu	Gene network reconstruction
BUScorrect	Xiangyu Luo	Batch Effects Correction with Unknown Subtypes
BUSpaRse	Lambda Moses	kallisto \| bustools R utilities
BUSseq	Fangda Song	Batch Effect Correction with Unknow Subtypes for scRNA-seq data
CAEN	Zhou Yan	Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
CAFE	Sander Bollen	Chromosmal Aberrations Finder in Expression data
CAGEfightR	Malte Thodberg	Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
cageminer	Fabrício Almeida-Silva	Candidate Gene Miner
CAGEr	Charles Plessy	Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
calm	Kun Liang	Covariate Assisted Large-scale Multiple testing
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
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
CARNIVAL	Olga Ivanova	A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
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	Automated functions for comparing various omic data from cbioportal.org
cBioPortalData	Marcel Ramos	Exposes and makes available data from the cBioPortal web resources
cbpManager	Arsenij Ustjanzew	Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics
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
celaref	Sarah Williams	Single-cell RNAseq cell cluster labelling by reference
celda	Joshua Campbell	CEllular Latent Dirichlet Allocation
CellaRepertorium	Andrew McDavid	Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
CellBarcode	Wenjie Sun	Cellular DNA Barcode Analysis toolkit
cellbaseR	Mohammed OE Abdallah	Querying annotation data from the high performance Cellbase web
CellBench	Shian Su	Construct Benchmarks for Single Cell Analysis Methods
cellHTS2	Joseph Barry	Analysis of cell-based screens - revised version of cellHTS
CelliD	Akira Cortal	Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis
cellity	Tomislav Ilicic	Quality Control for Single-Cell RNA-seq Data
CellMapper	Brad Nelms	Predict genes expressed selectively in specific cell types
cellmigRation	Waldir Leoncio	Track Cells, Analyze Cell Trajectories and Compute Migration Statistics
CellMixS	Almut Lütge	Evaluate Cellspecific Mixing
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
CellTrails	Daniel Ellwanger	Reconstruction, visualization and analysis of branching trajectories
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
censcyt	Reto Gerber	Differential abundance analysis with a right censored covariate in high-dimensional cytometry
Cepo	Hani Jieun Kim	Cepo for the identification of differentially stable genes
ceRNAnetsim	Selcen Ari Yuka	Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)
CeTF	Carlos Alberto Oliveira de Biagi Junior	Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
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
cfDNAPro	Haichao Wang	cfDNAPro Helps Characterise and Visualise Whole Genome Sequencing Data from Liquid Biopsy
CGEN	Justin Lee	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
ChemmineOB	Thomas Girke	R interface to a subset of OpenBabel functionalities
ChemmineR	Thomas Girke	Cheminformatics Toolkit for R
CHETAH	Jurrian de Kanter	Fast and accurate scRNA-seq cell type identification
ChIC	Carmen Maria Livi	Quality Control Pipeline for ChIP-Seq Data
Chicago	Mikhail Spivakov	CHiCAGO: Capture Hi-C Analysis of Genomic Organization
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	Jianhong Ou, Lihua Julie Zhu	Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
ChIPQC	Tom Carroll, Rory Stark	Quality metrics for ChIPseq data
ChIPseeker	Guangchuang Yu	ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
chipseq	Bioconductor Package Maintainer	chipseq: A package for analyzing chipseq data
ChIPseqR	Peter Humburg	Identifying Protein Binding Sites in High-Throughput Sequencing Data
ChIPsim	Peter Humburg	Simulation of ChIP-seq experiments
ChIPXpress	George Wu	ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
chopsticks	Hin-Tak Leung	The 'snp.matrix' and 'X.snp.matrix' Classes
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
ChromSCape	Pacome Prompsy	Analysis of single-cell epigenomics datasets with a Shiny App
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
cicero	Hannah Pliner	Precict cis-co-accessibility from single-cell chromatin accessibility data
CIMICE	Nicolò Rossi	CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
CINdex	Yuriy Gusev	Chromosome Instability Index
circRNAprofiler	Simona Aufiero	circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs
cisPath	Likun Wang	Visualization and management of the protein-protein interaction networks.
CiteFuse	Yingxin Lin	CiteFuse: multi-modal analysis of CITE-seq data
ClassifyR	Dario Strbenac	A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing
cleanUpdTSeq	Jianhong Ou ; Lihua Julie Zhu	cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data
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
cliProfiler	You Zhou	A package for the CLIP data visualization
cliqueMS	Oriol Senan Campos	Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
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
CluMSID	Tobias Depke	Clustering of MS2 Spectra for Metabolite Identification
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	A universal enrichment tool for interpreting omics data
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
clustifyr	Rui Fu	Classifier for Single-cell RNA-seq Using Cell Clusters
CMA	Roman Hornung	Synthesis of microarray-based classification
cmapR	Ted Natoli	CMap Tools in R
cn.farms	Andreas Mitterecker	cn.FARMS - factor analysis for copy number estimation
cn.mops	Gundula Povysil	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	E.Gjerga	Integration of CellNOptR to add missing links
CNORfuzzy	T. Cokelaer	Addon to CellNOptR: Fuzzy Logic
CNORode	Attila Gabor	ODE add-on to CellNOptR
CNTools	J. Zhang	Convert segment data into a region by sample matrix to allow for other high level computational analyses.
CNVfilteR	Jose Marcos Moreno-Cabrera	Identifies false positives of CNV calling tools by using SNV calls
CNVgears	Simone Montalbano	A Framework of Functions to Combine, Analize and Interpret CNVs Calling Results
cnvGSA	Joseph Lugo	Gene Set Analysis of (Rare) Copy Number Variants
CNViz	Rebecca Greenblatt	Copy Number Visualization
CNVPanelizer	Thomas Wolf	Reliable CNV detection in targeted sequencing applications
CNVRanger	Ludwig Geistlinger	Summarization and expression/phenotype association of CNV ranges
CNVrd2	Hoang Tan Nguyen	CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.
CoCiteStats	Bioconductor Package Maintainer	Different test statistics based on co-citation.
COCOA	John Lawson	Coordinate Covariation Analysis
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, Melanie L. Loth	Coordinated Gene Activity in Pattern Sets
cogena	Zhilong Jia	co-expressed gene-set enrichment analysis
Cogito	Annika Bürger	Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets
coGPS	Yingying Wei	cancer outlier Gene Profile Sets
COHCAP	Charles Warden	CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
cola	Zuguang Gu	A Framework for Consensus Partitioning
combi	Joris Meys	Compositional omics model based visual integration
coMET	Tiphaine Martin	coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
compartmap	Benjamin Johnson	Higher-order chromatin domain inference in single cells from scRNA-seq and scATAC-seq
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
ComplexHeatmap	Zuguang Gu	Make Complex Heatmaps
ComPrAn	Petra Palenikova	Complexome Profiling Analysis package
conclus	Ilyess Rachedi	ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion
condiments	Hector Roux de Bezieux	Differential Topology, Progression and Differentiation
CONFESS	Diana LOW	Cell OrderiNg by FluorEScence Signal
consensus	Tim Peters	Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
ConsensusClusterPlus	Matt Wilkerson	ConsensusClusterPlus
consensusDE	Ashley J. Waardenberg	RNA-seq analysis using multiple algorithms
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
CONSTANd	Dirk Valkenborg	Data normalization by matrix raking
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.
CopyNumberPlots	Bernat Gel	Create Copy-Number Plots using karyoploteR functionality
CopywriteR	Oscar Krijgsman	Copy number information from targeted sequencing using off-target reads
coRdon	Anamaria Elek	Codon Usage Analysis and Prediction of Gene Expressivity
CoRegNet	Remy Nicolle	CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoreGx	Benjamin Haibe-Kains	Classes and Functions to Serve as the Basis for Other 'Gx' Packages
Cormotif	Yingying Wei	Correlation Motif Fit
corral	Lauren Hsu	Correspondence Analysis for Single Cell Data
CORREP	Dongxiao Zhu	Multivariate Correlation Estimator and Statistical Inference Procedures.
coseq	Andrea Rau	Co-Expression Analysis of Sequencing Data
cosmiq	David Fischer	cosmiq - COmbining Single Masses Into Quantities
cosmosR	Katharina Zirngibl	COSMOS (Causal Oriented Search of Multi-Omic Space)
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
countsimQC	Charlotte Soneson	Compare Characteristic Features of Count Data Sets
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
csdR	Jakob Peder Pettersen	Differential gene co-expression
CSSP	Chandler Zuo	ChIP-Seq Statistical Power
CSSQ	Fan Lab at Georgia Institute of Technology	Chip-seq Signal Quantifier Pipeline
ctc	Antoine Lucas	Cluster and Tree Conversion.
CTDquerier	Xavier Escribà-Montagut	Package for CTDbase data query, visualization and downstream analysis
ctgGEM	USD Biomedical Engineering	Generating Tree Hierarchy Visualizations from Gene Expression Data
cTRAP	Nuno Saraiva-Agostinho	Identification of candidate causal perturbations from differential gene expression data
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.
customCMPdb	Yuzhu Duan	Customize and Query Compound Annotation Database
customProDB	Xiaojing Wang Bo Wen	Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
cyanoFilter	Oluwafemi Olusoji	Phytoplankton Population Identification using Cell Pigmentation and/or Complexity
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
CyTOFpower	Anne-Maud Ferreira	Power analysis for CyTOF experiments
CytoGLMM	Christof Seiler	Conditional Differential Analysis for Flow and Mass Cytometry Experiments
cytoKernel	Tusharkanti Ghosh	Differential expression using kernel-based score test
cytolib	Mike Jiang	C++ infrastructure for representing and interacting with the gated cytometry data
cytomapper	Nils Eling	Visualization of highly multiplexed imaging data in R
CytoML	Mike Jiang	A GatingML Interface for Cross Platform Cytometry Data Sharing
CytoTree	Yuting Dai	A Toolkit for Flow And Mass Cytometry Data
dada2	Benjamin Callahan	Accurate, high-resolution sample inference from amplicon sequencing data
dagLogo	Jianhong Ou	dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory
daMA	Jobst Landgrebe	Efficient design and analysis of factorial two-colour microarray data
DAMEfinder	Stephany Orjuela	Finds DAMEs - Differential Allelicly MEthylated regions
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
dasper	David Zhang	Detecting abberant splicing events from RNA-sequencing data
dcanr	Dharmesh D. Bhuva	Differential co-expression/association network analysis
dce	Kim Philipp Jablonski	Pathway Enrichment Based on Differential Causal Effects
dcGSA	Jiehuan sun	Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
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
dearseq	Boris P. Hejblum	Differential Expression Analysis for RNA-seq data through a robust variance component test
debCAM	Lulu Chen	Deconvolution by Convex Analysis of Mixtures
debrowser	Alper Kucukural	Interactive Differential Expresion Analysis Browser
DECIPHER	Erik Wright	Tools for curating, analyzing, and manipulating biological sequences
deco	Francisco Jose Campos Laborie	Decomposing Heterogeneous Cohorts using Omic Data Profiling
DEComplexDisease	Guofeng Meng	A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis
decompTumor2Sig	Rosario M. Piro	Decomposition of individual tumors into mutational signatures by signature refitting
DeconRNASeq	Ting Gong	Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
decontam	Benjamin Callahan	Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
deconvR	İrem B. Gündüz	Simulation and Deconvolution of Omic Profiles
decoupleR	Pau Badia-i-Mompel	decoupleR: Ensemble of computational methods to infer biological activities from omics data
DeepBlueR	Felipe Albrecht, Markus List	DeepBlueR
DeepPINCS	Dongmin Jung	Protein Interactions and Networks with Compounds based on Sequences using Deep Learning
deepSNV	Moritz Gerstung	Detection of subclonal SNVs in deep sequencing data.
DEFormats	Andrzej Oleś	Differential gene expression data formats converter
DegNorm	Ji-Ping Wang	DegNorm: degradation normalization for RNA-seq data
DEGraph	Laurent Jacob	Two-sample tests on a graph
DEGreport	Lorena Pantano	Report of DEG analysis
DEGseq	Likun Wang	Identify Differentially Expressed Genes from RNA-seq data
DelayedArray	Hervé Pagès	A unified framework for working transparently with on-disk and in-memory array-like datasets
DelayedDataFrame	Qian Liu	Delayed operation on DataFrame using standard DataFrame metaphor
DelayedMatrixStats	Peter Hickey	Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
DelayedRandomArray	Aaron Lun	Delayed Arrays of Random Values
DelayedTensor	Koki Tsuyuzaki	R package for sparse and out-of-core arithmetic and decomposition of Tensor
deltaCaptureC	Michael Shapiro	This Package Discovers Meso-scale Chromatin Remodeling from 3C Data
deltaGseg	Diana Low	deltaGseg
DeMAND	Jung Hoon Woo, Mariano Alvarez	DeMAND
DeMixT	Shaolong Cao, Peng Yang	Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
densvis	Alan O'Callaghan	Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction
DEP	Arne Smits	Differential Enrichment analysis of Proteomics data
DepecheR	Jakob Theorell	Determination of essential phenotypic elements of clusters in high-dimensional entities
DEqMS	Yafeng Zhu	a tool to perform statistical analysis of differential protein expression for quantitative 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
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
DEWSeq	bioinformatics team Hentze	Differential Expressed Windows Based on Negative Binomial Distribution
DExMA	Juan Antonio Villatoro-García	Differential Expression Meta-Analysis
DEXSeq	Alejandro Reyes	Inference of differential exon usage in RNA-Seq
DFP	Rodrigo Alvarez-Glez	Gene Selection
DIAlignR	Shubham Gupta	Dynamic Programming Based Alignment of MS2 Chromatograms
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
diffUTR	Pierre-Luc Germain	diffUTR: Streamlining differential exon and 3' UTR usage
diggit	Mariano J Alvarez	Inference of Genetic Variants Driving Cellular Phenotypes
Dino	Jared Brown	Normalization of Single-Cell mRNA Sequencing Data
dir.expiry	Aaron Lun	Managing Expiration for Cache Directories
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
DiscoRhythm	Matthew Carlucci	Interactive Workflow for Discovering Rhythmicity in Biological Data
distinct	Simone Tiberi	distinct: a method for differential analyses via hierarchical permutation tests
dittoSeq	Daniel Bunis	User Friendly Single-Cell and Bulk RNA Sequencing Visualization
divergence	Wikum Dinalankara, Luigi Marchionni	Divergence: Functionality for assessing omics data by divergence with respect to a baseline
dks	Jeffrey T. Leek	The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.
DMCFB	Farhad Shokoohi	Differentially Methylated Cytosines via a Bayesian Functional Approach
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
DNABarcodeCompatibility	Céline Trébeau	A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms
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
Doscheda	Bruno Contrino	A DownStream Chemo-Proteomics Analysis Pipeline
DOSE	Guangchuang Yu	Disease Ontology Semantic and Enrichment analysis
doseR	ake.vastermark	doseR
dpeak	Dongjun Chung	dPeak (Deconvolution of Peaks in ChIP-seq 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	Jonathan Griffiths	Utilities for Handling Single-Cell Droplet Data
drugTargetInteractions	Thomas Girke	Drug-Target Interactions
DrugVsDisease	j. Saez-Rodriguez	Comparison of disease and drug profiles using Gene set Enrichment Analysis
DSS	Hao Wu, Hao Feng	Dispersion shrinkage for sequencing data
dStruct	Krishna Choudhary	Identifying differentially reactive regions from RNA structurome profiling data
DTA	Bjoern Schwalb	Dynamic Transcriptome Analysis
dualKS	Eric J. Kort, Yarong Yang	Dual KS Discriminant Analysis and Classification
Dune	Hector Roux de Bezieux	Improving replicability in single-cell RNA-Seq cell type discovery
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
easier	Oscar Lapuente-Santana	Estimate Systems Immune Response from RNA-seq data
easyreporting	Dario Righelli	Helps creating report for improving Reproducible Computational Research
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
edge	John D. Storey, Andrew J. Bass	Extraction of Differential Gene Expression
edgeR	Yunshun Chen, Gordon Smyth, Aaron Lun, Mark Robinson	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
eisaR	Michael Stadler	Exon-Intron Split Analysis (EISA) in R
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
EnhancedVolcano	Kevin Blighe	Publication-ready volcano plots with enhanced colouring and labeling
enhancerHomologSearch	Jianhong Ou	Identification of putative mammalian orthologs to given enhancer
EnMCB	Xin Yu	Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models
ENmix	Zongli Xu	Quality control and analysis tools for Illumina DNA methylation 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
enrichTF	Zheng Wei	Transcription Factors Enrichment Analysis
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
epialleleR	Oleksii Nikolaienko	Fast, Epiallele-Aware Methylation Reporter
epidecodeR	Kandarp Joshi	epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation
EpiDISH	Shijie C. Zheng	Epigenetic Dissection of Intra-Sample-Heterogeneity
epigenomix	Hans-Ulrich Klein	Epigenetic and gene transcription data normalization and integration with mixture models
epigraHMM	Pedro Baldoni	Epigenomic R-based analysis with hidden Markov models
epihet	Xiaowen Chen	Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
epiNEM	Martin Pirkl	epiNEM
epistack	DEVAILLY Guillaume	Heatmaps of Stack Profiles from Epigenetic Signals
EpiTxDb	Felix G.M. Ernst	Storing and accessing epitranscriptomic information using the AnnotationDbi interface
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
ERSSA	Zixuan Shao	Empirical RNA-seq Sample Size Analysis
esATAC	Zheng Wei	An Easy-to-use Systematic pipeline for ATACseq data analysis
escape	Nick Borcherding	Easy single cell analysis platform for enrichment
esetVis	Laure Cougnaud	Visualizations of expressionSet Bioconductor object
eudysbiome	Xiaoyuan Zhou	Cartesian plot and contingency test on 16S Microbial data
evaluomeR	José Antonio Bernabé-Díaz	Evaluation of Bioinformatics Metrics
EventPointer	Juan A. Ferrer-Bonsoms	An effective identification of alternative splicing events using junction arrays and RNA-Seq data
EWCE	Alan Murphy	Expression Weighted Celltype Enrichment
ExCluster	R. Matthew Tanner	ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition
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
exomePeak2	Zhen Wei	Bias-aware Peak Calling and Quantification for MeRIP-Seq
ExperimentHub	Bioconductor Package Maintainer	Client to access ExperimentHub resources
ExperimentHubData	Bioconductor Package Maintainer	Add resources to ExperimentHub
ExperimentSubset	Irzam Sarfraz	Manages subsets of data with Bioconductor Experiment objects
ExploreModelMatrix	Charlotte Soneson	Graphical Exploration of Design Matrices
ExpressionAtlas	Pedro Madrigal	Download datasets from EMBL-EBI Expression Atlas
fabia	Andreas Mitterecker	FABIA: Factor Analysis for Bicluster Acquisition
factDesign	Denise Scholtens	Factorial designed microarray experiment analysis
FamAgg	Johannes Rainer	Pedigree Analysis and Familial Aggregation
famat	Mathieu Charles	Functional analysis of metabolic and transcriptomic data
farms	Djork-Arne Clevert	FARMS - Factor Analysis for Robust Microarray Summarization
fastLiquidAssociation	Tina Gunderson	functions for genome-wide application of Liquid Association
FastqCleaner	Leandro Roser	A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
fastseg	Guenter Klambauer	fastseg - a fast segmentation algorithm
FCBF	Tiago Lubiana	Fast Correlation Based Filter for Feature Selection
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
fcoex	Tiago Lubiana	FCBF-based Co-Expression Networks for Single Cells
fcScan	Pierre Khoueiry Abdullah El-Kurdi	fcScan for detecting clusters of coordinates with user defined options
fdrame	Effi Kenigsberg	FDR adjustments of Microarray Experiments (FDR-AME)
FEAST	Kenong Su	FEAture SelcTion (FEAST) for Single-cell clustering
fedup	Catherine Ross	Fisher's Test for Enrichment and Depletion of User-Defined Pathways
FELLA	Sergio Picart-Armada	Interpretation and enrichment for metabolomics data
ffpe	Levi Waldron	Quality assessment and control for FFPE microarray expression data
fgga	Spetale Flavio	Hierarchical ensemble method based on factor graph
FGNet	Sara Aibar	Functional Gene Networks derived from biological enrichment analyses
fgsea	Alexey Sergushichev	Fast Gene Set Enrichment Analysis
FilterFFPE	Lanying Wei	FFPE Artificial Chimeric Read Filter for NGS data
FindIT2	Guandong Shang	find influential TF and Target based on multi-omics data
FindMyFriends	Thomas Lin Pedersen	Microbial Comparative Genomics in R
FISHalyseR	Karesh Arunakirinathan, Andreas Heindl	FISHalyseR a package for automated FISH quantification
fishpond	Michael Love	Fishpond: differential transcript and gene expression with inferential replicates
FitHiC	Ruyu Tan	Confidence estimation for intra-chromosomal contact maps
flagme	Mark Robinson, Riccardo Romoli	Analysis of Metabolomics GC/MS Data
FLAMES	Voogd Oliver	FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
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	Mike Jiang	flowCore: Basic structures for flow cytometry data
flowCut	Justin Meskas	Precise and Accurate Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis
flowCyBar	Joachim Schumann	Analyze flow cytometric data using gate information
flowDensity	Mehrnoush Malek	Sequential Flow Cytometry Data Gating
flowFP	Herb Holyst	Fingerprinting for Flow Cytometry
flowGraph	Alice Yue	Identifying differential cell populations in flow cytometry data accounting for marker frequency
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
FlowSOM	Sofie Van Gassen	Using self-organizing maps for visualization and interpretation of cytometry data
flowSpecs	Jakob Theorell	Tools for processing of high-dimensional cytometry data
flowStats	Greg Finak, Mike Jiang, Jake Wagner	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
flowUtils	Josef Spidlen	Utilities for flow cytometry
flowViz	Mike Jiang, Jake Wagner	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 gated and ungated cytometry data sets.
fmcsR	Thomas Girke	Mismatch Tolerant Maximum Common Substructure Searching
fmrs	Farhad Shokoohi	Variable Selection in Finite Mixture of AFT Regression and FMR
fobitools	Pol Castellano-Escuder	Tools For Manipulating FOBI Ontology
FoldGO	Daniil Wiebe	Package for Fold-specific GO Terms Recognition
FRASER	Christian Mertes	Find RAre Splicing Events in RNA-Seq Data
frenchFISH	Adam Berman	Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections
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
FScanR	Xiao Chen	Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output
FunChIP	Alice Parodi	Clustering and Alignment of ChIP-Seq peaks based on their shapes
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.
GAPGOM	Rezvan Ehsani	GAPGOM (novel Gene Annotation Prediction and other GO Metrics)
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
gcapc	Mingxiang Teng	GC Aware Peak Caller
gcatest	Wei Hao, John D. Storey	Genotype Conditional Association TEST
gCrisprTools	Russell Bainer	Suite of Functions for Pooled Crispr Screen QC and Analysis
gcrma	Z. Wu	Background Adjustment Using Sequence Information
GCSConnection	Jiefei Wang	Creating R Connection with Google Cloud Storage
GCSFilesystem	Jiefei Wang	Mounting a Google Cloud bucket to a local directory
GCSscore	Guy M. Harris	GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays
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
GEM	Hong Pan	GEM: fast association study for the interplay of Gene, Environment and Methylation
gemini	Sidharth Jain	GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens
genArise	IFC Development Team	Microarray Analysis tool
genbankr	Gabriel Becker	Parsing GenBank files into semantically useful objects
GeneAccord	Ariane L. Moore	Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients
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	Gene Expression Signature based Similarity Metric
genefilter	Bioconductor Package Maintainer	genefilter: methods for filtering genes from high-throughput experiments
genefu	Benjamin Haibe-Kains	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	Tools for Testing Gene-Gene Interaction at the Gene Level
GeneMeta	Bioconductor Package Maintainer	MetaAnalysis for High Throughput Experiments
GeneNetworkBuilder	Jianhong Ou	GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data
GeneOverlap	Antnio Miguel de Jesus Domingues, Max-Planck Institute for Cell Biology and Genetics	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
GENESIS	Stephanie M. Gogarten	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
GeneticsPed	David Henderson	Pedigree and genetic relationship functions
GeneTonic	Federico Marini	Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
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
GenomeInfoDb	Bioconductor Package Maintainer	Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
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
GenomicDistributions	Kristyna Kupkova	GenomicDistributions: fast analysis of genomic intervals with Bioconductor
GenomicFeatures	Bioconductor Package Maintainer	Conveniently import and query gene models
GenomicFiles	Bioconductor Package Maintainer	Distributed computing by file or by range
genomicInstability	Mariano Alvarez	Genomic Instability estimation for scRNA-Seq
GenomicInteractions	Liz Ing-Simmons	Utilities for handling genomic interaction data
GenomicOZone	Hua Zhong, Mingzhou Song	Delineate outstanding genomic zones of differential gene activity
GenomicRanges	Bioconductor Package Maintainer	Representation and manipulation of genomic intervals
GenomicScores	Robert Castelo	Infrastructure to work with genomewide position-specific scores
GenomicSuperSignature	Sehyun Oh	Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
GenomicTuples	Peter Hickey	Representation and Manipulation of Genomic Tuples
genotypeeval	Jennifer Tom	QA/QC of a gVCF or VCF file
genphen	Simo Kitanovski	genphen: tool for quantification of genotype-phenotype associations in genome wide association studies (GWAS)
GenVisR	Zachary Skidmore	Genomic Visualizations in R
GeoDiff	Zhi Yang	Count model based differential expression and normalization on GeoMx RNA data
GEOexplorer	Guy Hunt	GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation
GEOfastq	Alex Pickering	Downloads ENA Fastqs With GEO Accessions
GEOmetadb	Jack Zhu	A compilation of metadata from NCBI GEO
GeomxTools	Nicole Ortogero	NanoString GeoMx Tools
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
getDEE2	Mark Ziemann	Programmatic access to the DEE2 RNA expression dataset
geva	Itamar José Guimarães Nunes	Gene Expression Variation Analysis (GEVA)
GEWIST	Wei Q. Deng	Gene Environment Wide Interaction Search Threshold
ggbio	Michael Lawrence	Visualization tools for genomic data
ggcyto	Mike Jiang,Jake Wagner	Visualize Cytometry data with ggplot
ggmsa	Lang Zhou	Plot Multiple Sequence Alignment using 'ggplot2'
GGPA	Dongjun Chung	graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
ggspavis	Lukas M. Weber	Visualization functions for spatially resolved transcriptomics data
ggtree	Guangchuang Yu	an R package for visualization of tree and annotation data
ggtreeExtra	Shuangbin Xu	An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"
GIGSEA	Shijia Zhu	Genotype Imputed Gene Set Enrichment Analysis
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
GladiaTOX	PMP S.A. R Support	R Package for Processing High Content Screening data
Glimma	Shian Su	Interactive HTML graphics
glmGamPoi	Constantin Ahlmann-Eltze	Fit a Gamma-Poisson Generalized Linear Model
glmSparseNet	André Veríssimo	Network Centrality Metrics for Elastic-Net Regularized Models
GlobalAncova	Manuela Hummel	Global test for groups of variables via model comparisons
globalSeq	Armin Rauschenberger	Global Test for Counts
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
GmicR	Richard Virgen-Slane	Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
gmoviz	Kathleen Zeglinski	Seamless visualization of complex genomic variations in GMOs and edited cell lines
GMRP	Yuan-De Tan	GWAS-based Mendelian Randomization and Path Analyses
GNET2	Chen Chen	Constructing gene regulatory networks from expression data through functional module inference
GOexpress	Kevin Rue-Albrecht	Visualise microarray and RNAseq data using gene ontology annotations
GOfuncR	Steffi Grote	Gene ontology enrichment using FUNC
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	Matthew Young, Nadia Davidson	Gene Ontology analyser for RNA-seq and other length biased data
GOSim	Holger Froehlich	Computation of functional similarities between GO terms and gene products; GO enrichment analysis
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
GPA	Dongjun Chung	GPA (Genetic analysis incorporating Pleiotropy and Annotation)
gpart	Sun Ah Kim	Human genome partitioning of dense sequencing data by identifying haplotype blocks
gpls	Bioconductor Package Maintainer	Classification using generalized partial least squares
gprege	Alfredo Kalaitzis	Gaussian Process Ranking and Estimation of Gene Expression time-series
gpuMagic	Jiefei Wang	An openCL compiler with the capacity to compile R functions and run the code on GPU
gramm4R	Tianlu Chen	Generalized correlation analysis and model construction strategy for metabolome and microbiome
granulator	Sabina Pfister	Rapid benchmarking of methods for in silico deconvolution of bulk RNA-seq data
graper	Britta Velten	Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes
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
gscreend	Katharina Imkeller	Analysis of pooled genetic screens
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
GSEAmining	Oriol Arqués	Make Biological Sense of Gene Set Enrichment Analysis Outputs
gsean	Dongmin Jung	Gene Set Enrichment Analysis with Networks
GSgalgoR	Carlos Catania	An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer
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
GWAS.BAYES	Jake Williams	GWAS for Selfing Species
gwascat	VJ Carey	representing and modeling data in the EMBL-EBI GWAS catalog
GWASTools	Stephanie M. Gogarten	Tools for Genome Wide Association Studies
gwasurvivr	Abbas Rizvi	gwasurvivr: an R package for genome wide survival analysis
GWENA	Gwenaëlle Lemoine	Pipeline for augmented co-expression analysis
h5vc	Paul Theodor Pyl	Managing alignment tallies using a hdf5 backend
hapFabia	Andreas Mitterecker	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
hca	Martin Morgan	Exploring the Human Cell Atlas Data Coordinating Platform
HDF5Array	Hervé Pagès	HDF5 backend 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
Herper	Thomas Carroll	The Herper package is a simple toolset to install and manage conda packages and environments from R
HGC	XGlab	A fast hierarchical graph-based clustering method
hiAnnotator	Nirav V Malani	Functions for annotating GRanges objects
HIBAG	Xiuwen Zheng	HLA Genotype Imputation with Attribute Bagging
HiCBricks	Koustav Pal	Framework for Storing and Accessing Hi-C Data Through HDF Files
HiCcompare	John Stansfield, Mikhail Dozmorov	HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
HiCDCPlus	Merve Sahin	Hi-C Direct Caller Plus
hierGWAS	Laura Buzdugan	Asessing statistical significance in predictive GWA studies
hierinf	Claude Renaux	Hierarchical Inference
HilbertCurve	Zuguang Gu	Making 2D Hilbert Curve
HilbertVis	Simon Anders	Hilbert curve visualization
HilbertVisGUI	Simon Anders	HilbertVisGUI
HiLDA	Zhi Yang	Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation
hipathia	Marta R. Hidalgo	HiPathia: High-throughput Pathway Analysis
HIPPO	Tae Kim	Heterogeneity-Induced Pre-Processing tOol
hiReadsProcessor	Nirav V Malani	Functions to process LM-PCR reads from 454/Illumina data
HIREewas	Xiangyu Luo	Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies
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)
HPAanalyze	Anh Nhat Tran	Retrieve and analyze data from the Human Protein Atlas
hpar	Laurent Gatto	Human Protein Atlas in R
HPAStainR	Tim O. Nieuwenhuis	Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes
HPiP	Matineh Rahmatbakhsh	Host-Pathogen Interaction Prediction
HTqPCR	Heidi Dvinge	Automated analysis of high-throughput qPCR data
HTSeqGenie	Jens Reeder	A NGS analysis pipeline.
HTSFilter	Andrea Rau	Filter replicated high-throughput transcriptome sequencing data
HubPub	Kayla Interdonato	Utilities to create and use Bioconductor Hubs
HumanTranscriptomeCompendium	VJ Carey	Tools to work with a Compendium of 181000 human transcriptome sequencing studies
hummingbird	Eleni Adam	Bayesian Hidden Markov Model for the detection of differentially methylated regions
HybridMTest	Demba Fofana	Hybrid Multiple Testing
hypeR	Anthony Federico	An R Package For Geneset Enrichment Workflows
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
iasva	Donghyung Lee, Anthony Cheng	Iteratively Adjusted Surrogate Variable Analysis
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
icetea	Vivek Bhardwaj	Integrating Cap Enrichment with Transcript Expression Analysis
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
idpr	William M. McFadden	Profiling and Analyzing Intrinsically Disordered Proteins in R
idr2d	Konstantin Krismer	Irreproducible Discovery Rate for Genomic Interactions Data
iGC	Liang-Bo Wang	An integrated analysis package of Gene expression and Copy number alteration
IgGeneUsage	Simo Kitanovski	Differential gene usage in immune repertoires
igvR	Paul Shannon	igvR: integrative genomics viewer
IHW	Nikos Ignatiadis	Independent Hypothesis Weighting
illuminaio	Kasper Daniel Hansen	Parsing Illumina Microarray Output Files
ILoReg	Johannes Smolander	ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
imageHTS	Joseph Barry	Analysis of high-throughput microscopy-based screens
IMAS	Seonggyun Han	Integrative analysis of Multi-omics data for Alternative Splicing
imcRtools	Nils Eling	Methods for imaging mass cytometry data analysis
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
immunotation	Katharina Imkeller	Tools for working with diverse immune genes
IMPCdata	Jeremy Mason	Retrieves data from IMPC database
impute	Balasubramanian Narasimhan	impute: Imputation for microarray data
INDEED	Ressom group, Yiming Zuo	Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
infercnv	Christophe Georgescu	Infer Copy Number Variation from Single-Cell RNA-Seq Data
infinityFlow	Etienne Becht	Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions
Informeasure	Chu Pan	R implementation of Information measures
InPAS	Jianhong Ou	A Bioconductor package for identifying novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
INPower	Bill Wheeler	An R package for computing the number of susceptibility SNPs
INSPEcT	Stefano de Pretis, Mattia Furlan	Modeling RNA synthesis, processing and degradation with RNA-seq data
InTAD	Konstantin Okonechnikov	Search for correlation between epigenetic signals and gene expression in TADs
intansv	Wen Yao	Integrative analysis of structural variations
interacCircos	Zhe Cui	The Generation of Interactive Circos Plot
InteractionSet	Aaron Lun	Base Classes for Storing Genomic Interaction Data
InteractiveComplexHeatmap	Zuguang Gu	Make Interactive Complex Heatmaps
interactiveDisplay	Bioconductor Package Maintainer	Package for enabling powerful shiny web displays of Bioconductor objects
interactiveDisplayBase	Bioconductor Package Maintainer	Base package for enabling powerful shiny web displays of Bioconductor objects
InterCellar	Marta Interlandi	InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics
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
iPath	Kenong Su	iPath pipeline for detecting perturbed pathways at individual level
ipdDb	Steffen Klasberg	IPD IMGT/HLA and IPD KIR database for Homo sapiens
IPO	Thomas Riebenbauer	Automated Optimization of XCMS Data Processing parameters
IRanges	Bioconductor Package Maintainer	Foundation of integer range manipulation in Bioconductor
IRISFGM	Yuzhou Chang	Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq
ISAnalytics	Andrea Calabria	Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies
iSEE	Kevin Rue-Albrecht	Interactive SummarizedExperiment Explorer
iSEEu	Kevin Rue-Albrecht	iSEE Universe
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
IsoCorrectoR	Christian Kohler	Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments
IsoCorrectoRGUI	Christian Kohler	Graphical User Interface for IsoCorrectoR
IsoformSwitchAnalyzeR	Kristoffer Vitting-Seerup	Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read 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
karyoploteR	Bernat Gel	Plot customizable linear genomes displaying arbitrary data
KBoost	Luis F. Iglesias-Martinez	Inference of gene regulatory networks from gene expression 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
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 the Kyoto Encyclopedia of Genes and Genomes (KEGG)
KinSwingR	Ashley J. Waardenberg	KinSwingR: network-based kinase activity prediction
kissDE	Aurélie Siberchicot	Retrieves Condition-Specific Variants in RNA-Seq Data
KnowSeq	Daniel Castillo-Secilla	KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
LACE	Davide Maspero	Longitudinal Analysis of Cancer Evolution (LACE)
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	Olivier Francois, Eric Frichot	LEA: an R package for Landscape and Ecological Association Studies
LedPred	Aitor Gonzalez	Learning from DNA to Predict Enhancers
lefser	Asya Khleborodova	R implementation of the LEfSE method for microbiome biomarker discovery
les	Julian Gehring	Identifying Differential Effects in Tiling Microarray Data
levi	Jose Luiz Rybarczyk Filho	Landscape Expression Visualization Interface
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
LineagePulse	David S Fischer	Differential expression analysis and model fitting for single-cell RNA-seq data
LinkHD	"Laura M Zingaretti"	LinkHD: a versatile framework to explore and integrate heterogeneous data
Linnorm	Ken Shun Hang Yip	Linear model and normality based normalization and transformation method (Linnorm)
lionessR	Ping-Han Hsieh	Modeling networks for individual samples using LIONESS
lipidr	Ahmed Mohamed	Data Mining and Analysis of Lipidomics Datasets
LiquidAssociation	Yen-Yi Ho	LiquidAssociation
lisaClust	Ellis Patrick	lisaClust: Clustering of Local Indicators of Spatial Association
lmdme	Cristobal Fresno	Linear Model decomposition for Designed Multivariate Experiments
LOBSTAHS	Henry Holm, Daniel Lowenstein, 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
LOLA	Nathan Sheffield	Locus overlap analysis for enrichment of genomic ranges
LoomExperiment	Bioconductor Package Maintainer	LoomExperiment container
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
LRBaseDbi	Koki Tsuyuzaki	DBI to construct LRBase-related package
LRcell	Wenjing Ma	Differential cell type change analysis using Logistic/linear Regression
lumi	Lei Huang	BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
LymphoSeq	David Coffey	Analyze high-throughput sequencing of T and B cell receptors
M3C	Christopher John	Monte Carlo Reference-based Consensus Clustering
M3Drop	Tallulah Andrews	Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
m6Aboost	You Zhou	m6Aboost
maanova	Keith Sheppard	Tools for analyzing Micro Array experiments
Maaslin2	Lauren McIver	"Multivariable Association Discovery in Population-scale Meta-omics Studies"
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
MACSQuantifyR	Raphaël Bonnet	Fast treatment of MACSQuantify FACS data
MACSr	Qiang Hu	MACS: Model-based Analysis for ChIP-Seq
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
MAGAR	Michael Scherer	MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
MAGeCKFlute	Wubing Zhang	Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
MAI	Jonathan Dekermanjian	Mechanism-Aware Imputation
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
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
marr	Tusharkanti Ghosh	Maximum rank reproducibility
marray	Yee Hwa (Jean) Yang	Exploratory analysis for two-color spotted microarray data
martini	Hector Climente-Gonzalez	GWAS Incorporating Networks
maser	Diogo F.T. Veiga	Mapping Alternative Splicing Events to pRoteins
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	Sergio Oller	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.
MatrixGenerics	Peter Hickey	S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
MatrixQCvis	Thomas Naake	Shiny-based interactive data-quality exploration for omics data
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 file-based data structures
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)
mbkmeans	Davide Risso	Mini-batch K-means Clustering for Single-Cell RNA-seq
mBPCR	P.M.V. Rancoita	Bayesian Piecewise Constant Regression for DNA copy number estimation
MBQN	Eva Brombacher	Mean/Median-balanced quantile normalization
MBttest	Yuan-De Tan	Multiple Beta t-Tests
MCbiclust	Robert Bentham	Massive correlating biclusters for gene expression data and associated methods
mCSEA	Jordi Martorell-Marugán	Methylated CpGs Set Enrichment 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	Xavier Escribà Montagut	Perform methylation analysis
MeasurementError.cor	Beiying Ding	Measurement Error model estimate for correlation coefficient
MEAT	Sarah Voisin	Muscle Epigenetic Age Test
MEB	Jiadi Zhu, Yan Zhou	A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq data
MEDIPS	Lukas Chavez	DNA IP-seq data analysis
MEDME	Mattia Pelizzola	Modelling Experimental Data from MeDIP Enrichment
megadepth	David Zhang	megadepth: BigWig and BAM related utilities
MEIGOR	Jose A. Egea	MEIGO - MEtaheuristics for bIoinformatics Global Optimization
Melissa	C. A. Kapourani	Bayesian clustering and imputationa of single cell methylomes
memes	Spencer Nystrom	motif matching, comparison, and de novo discovery using the MEME Suite
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
MesKit	Mengni Liu	A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations
messina	Mark Pinese	Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems
Metab	Raphael Aggio	Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
metabCombiner	Hani Habra	Method for Combining LC-MS Metabolomics Feature Measurements
MetaboCoreUtils	Johannes Rainer	Core Utils for Metabolomics Data
metabolomicsWorkbenchR	Gavin Rhys Lloyd	Metabolomics Workbench in R
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
metagene2	Eric Fournier	A package to produce metagene plots
metagenomeSeq	Joseph N. Paulson	Statistical analysis for sparse high-throughput sequencing
metahdep	John R. Stevens	Hierarchical Dependence in Meta-Analysis
metaMS	Yann Guitton	MS-based metabolomics annotation pipeline
MetaNeighbor	Stephan Fischer	Single cell replicability analysis
metapod	Aaron Lun	Meta-Analyses on P-Values of Differential Analyses
metapone	Tianwei Yu	Conducts pathway test of metabolomics data using a weighted permutation test
metaSeq	Koki Tsuyuzaki	Meta-analysis of RNA-Seq count data in multiple studies
metaseqR2	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
MetaVolcanoR	Cesar Prada	Gene Expression Meta-analysis Visualization Tool
MetCirc	Thomas Naake	Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
MethCP	Boying Gong	Differential methylation anlsysis for bisulfite sequencing 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
MethReg	Tiago Silva	Assessing the regulatory potential of DNA methylation regions or sites on gene transcription
methrix	Anand Mayakonda	Fast and efficient summarization of generic bedGraph files from Bisufite sequencing
MethTargetedNGS	Muhammad Ahmer Jamil	Perform Methylation Analysis on Next Generation Sequencing Data
MethylAid	L.J.Sinke	Visual and interactive quality control of large Illumina DNA Methylation array data sets
methylCC	Stephanie C. Hicks	Estimate the cell composition of whole blood in DNA methylation samples
methylclock	Dolors Pelegri-Siso	Methylclock - DNA methylation-based clocks
methylGSA	Xu Ren	Gene Set Analysis Using the Outcome of Differential Methylation
methylInheritance	Astrid Deschênes	Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations 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
methylscaper	Bacher Rhonda	Visualization of Methylation Data
MethylSeekR	Lukas Burger	Segmentation of Bis-seq data
methylSig	Raymond G. Cavalcante	MethylSig: Differential Methylation Testing for WGBS and RRBS Data
methylumi	Sean Davis	Handle Illumina methylation data
MetID	Zhenzhi Li	Network-based prioritization of putative metabolite IDs
MetNet	Thomas Naake	Inferring metabolic networks from untargeted high-resolution mass spectrometry data
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
mia	Felix G.M. Ernst	Microbiome analysis
miaSim	Yagmur Simsek	Microbiome Data Simulation
miaViz	Felix G.M. Ernst	Microbiome Analysis Plotting and Visualization
MiChip	Jonathon Blake	MiChip Parsing and Summarizing Functions
microbiome	Leo Lahti	Microbiome Analytics
microbiomeDASim	Justin Williams	Microbiome Differential Abundance Simulation
microbiomeExplorer	Janina Reeder	Microbiome Exploration App
microbiomeMarker	Yang Cao	microbiome biomarker analysis toolkit
MicrobiomeProfiler	Meijun Chen	An R/shiny package for microbiome functional enrichment analysis
MicrobiotaProcess	Shuangbin Xu	A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
microRNA	"James F. Reid"	Data and functions for dealing with microRNAs
midasHLA	Maciej Migdał	R package for immunogenomics data handling and association analysis
MIGSA	Juan C. Rodriguez	Massive and Integrative Gene Set Analysis
miloR	Mike Morgan	Differential neighbourhood abundance testing on a graph
mimager	Aaron Wolen	mimager: The Microarray Imager
MIMOSA	Greg Finak	Mixture Models for Single-Cell Assays
mina	Rui Guan	Microbial community dIversity and Network Analysis
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 Scharpf	A Package for De Novo CNV Detection in Case-Parent Trios
MiPP	Sukwoo Kim	Misclassification Penalized Posterior Classification
miQC	Ariel Hippen	Flexible, probabilistic metrics for quality control of scRNA-seq data
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	Vu Viet Hoang Pham	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	T. Ian Simpson	miRNAtap: microRNA Targets - Aggregated Predictions
miRSM	Junpeng Zhang	Inferring miRNA sponge modules in heterogeneous data
miRspongeR	Junpeng Zhang	Identification and analysis of miRNA sponge interaction networks and modules
mirTarRnaSeq	Mercedeh Movassagh	mirTarRnaSeq
missMethyl	Belinda Phipson, Jovana Maksimovic, Andrew Lonsdale	Analysing Illumina HumanMethylation BeadChip Data
missRows	Gonzalez Ignacio	Handling Missing Individuals in Multi-Omics Data Integration
mistyR	Jovan Tanevski	Multiview Intercellular SpaTial modeling framework
mitch	Mark Ziemann	Multi-Contrast Gene Set Enrichment Analysis
mitoClone2	Benjamin Story	Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations
mixOmics	Al J Abadi	Omics Data Integration Project
MLInterfaces	V. Carey	Uniform interfaces to R machine learning procedures for data in Bioconductor containers
MLP	Tobias Verbeke	Mean Log P Analysis
MLSeq	Gokmen Zararsiz	Machine Learning Interface for RNA-Seq Data
MMAPPR2	Jonathon Hill	Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
MMDiff2	Gabriele Schweikert	Statistical Testing for ChIP-Seq data sets
MMUPHin	Siyuan MA	Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies
mnem	Martin Pirkl	Mixture Nested Effects Models
moanin	Nelle Varoquaux	An R Package for Time Course RNASeq Data Analysis
MODA	Dong Li	MODA: MOdule Differential Analysis for weighted gene co-expression network
ModCon	Johannes Ptok	Modifying splice site usage by changing the mRNP code, while maintaining the genetic code
Modstrings	Felix G.M. Ernst	Working with modified nucleotide sequences
MOFA2	Britta Velten	Multi-Omics Factor Analysis v2
MOGAMUN	Elva-María Novoa-del-Toro	MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
mogsa	Chen Meng	Multiple omics data integrative clustering and gene set analysis
MOMA	Sunny Jones	Multi Omic Master Regulator Analysis
monaLisa	Michael Stadler	Binned Motif Enrichment Analysis and Visualization
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
mosaics	Dongjun Chung	MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
mosbi	Tim Daniel Rose	Molecular Signature identification using Biclustering
MOSim	Carlos Martínez	Multi-Omics Simulation (MOSim)
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
motifStack	Jianhong Ou	Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
MouseFM	Matthias Munz	In-silico methods for genetic finemapping in inbred mice
MPFE	Conrad Burden	Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data
mpra	Leslie Myint	Analyze massively parallel reporter assays
MPRAnalyze	Tal Ashuach	Statistical Analysis of MPRA data
MQmetrics	Alvaro Sanchez-Villalba	Quality Control of Protemics Data
msa	Ulrich Bodenhofer	Multiple Sequence Alignment
MsBackendMassbank	RforMassSpectrometry Package Maintainer	Mass Spectrometry Data Backend for MassBank record Files
MsBackendMgf	RforMassSpectrometry Package Maintainer	Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files
MsBackendRawFileReader	Christian Panse	Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
MsCoreUtils	RforMassSpectrometry Package Maintainer	Core Utils for Mass Spectrometry Data
MsFeatures	Johannes Rainer	Functionality for Mass Spectrometry Features
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+
msImpute	Soroor Hediyeh-zadeh	Imputation of label-free mass spectrometry peptides
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
MSPrep	Max McGrath	Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data
msPurity	Thomas N. Lawson	Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
msqrob2	Lieven Clement	Robust statistical inference for quantitative LC-MS proteomics
MSstats	Meena Choi	Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
MSstatsConvert	Mateusz Staniak	Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format
MSstatsLiP	Devon Kohler	LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
MSstatsLOBD	Devon Kohler	Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)
MSstatsPTM	Devon Kohler	Statistical Characterization of Post-translational Modifications
MSstatsQC	Eralp Dogu	Longitudinal system suitability monitoring and quality control for proteomic experiments
MSstatsQCgui	Eralp Dogu	A graphical user interface for MSstatsQC package
MSstatsSampleSize	Ting Huang	Simulation tool for optimal design of high-dimensional MS-based proteomics experiment
MSstatsTMT	Ting Huang	Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
MSstatsTMTPTM	Devon Kohler	Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Mulcom	Claudio Isella	Calculates Mulcom test
MultiAssayExperiment	Marcel Ramos	Software for the integration of multi-omics experiments in Bioconductor
MultiBaC	Manuel Ugidos	Multiomic Batch effect Correction
multiClust	Nathan Lawlor	multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
multicrispr	Aditya Bhagwat	Multi-locus multi-purpose Crispr/Cas design
MultiDataSet	Xavier Escrib Montagut	Implementation of MultiDataSet and ResultSet
multiGSEA	Sebastian Canzler	Combining GSEA-based pathway enrichment with multi omics data integration
multiHiCcompare	John Stansfield, Mikhail Dozmorov	Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
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
multiSight	Florian Jeanneret	Multi-omics Classification, Functional Enrichment and Network Inference analysis
multtest	Katherine S. Pollard	Resampling-based multiple hypothesis testing
mumosa	Aaron Lun	Multi-Modal Single-Cell Analysis Methods
MungeSumstats	Alan Murphy	Standardise summary statistics from GWAS
muscat	Helena L. Crowell	Multi-sample multi-group scRNA-seq data analysis tools
muscle	Alex T. Kalinka	Multiple Sequence Alignment with MUSCLE
musicatk	Aaron Chevalier	Mutational Signature Comprehensive Analysis Toolkit
MutationalPatterns	Mark van Roosmalen	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	Laurent Gatto	An mzIdentML parser for R
mzR	Steffen Neumann, Laurent Gatto, Qiakng 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
NanoMethViz	Shian Su	Visualise methlation data from Oxford Nanopore sequencing
NanoStringDiff	tingting zhai,hong wang	Differential Expression Analysis of NanoString nCounter Data
NanoStringNCTools	Nicole Ortogero	NanoString nCounter Tools
NanoStringQCPro	Robert Ziman	Quality metrics and data processing methods for NanoString mRNA gene expression data
nanotatoR	Surajit Bhattacharya	Next generation structural variant annotation and classification
NanoTube	Caleb Class	An Easy Pipeline for NanoString nCounter Data Analysis
NBAMSeq	Xu Ren	Negative Binomial Additive Model for RNA-Seq Data
NBSplice	Gabriela Merino	Negative Binomial Models to detect Differential Splicing
ncdfFlow	Mike Jiang, Jake Wagner	ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
ncGTW	Chiung-Ting Wu	Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection
NCIgraph	Laurent Jacob	Pathways from the NCI Pathways Database
ncRNAtools	Lara Selles Vidal	An R toolkit for non-coding RNA
ndexr	Florian Auer	NDEx R client library
nearBynding	Veronica Busa	Discern RNA structure proximal to protein binding
Nebulosa	Jose Alquicira-Hernandez	Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation
NeighborNet	Sahar Ansari	Neighbor_net analysis
nempi	Martin Pirkl	Inferring unobserved perturbations from gene expression data
netbiov	Shailesh tripathi	A package for visualizing complex biological network
netboost	Pascal Schlosser	Network Analysis Supported by Boosting
netboxr	Eirc Minwei Liu	netboxr
netDx	Shraddha Pai	Network-based patient classifier
nethet	Nicolas Staedler, Frank Dondelinger	A bioconductor package for high-dimensional exploration of biological network heterogeneity
netOmics	Antoine Bodein	Multi-Omics (time-course) network-based integration and interpretation
NetPathMiner	Ahmed Mohamed	NetPathMiner for Biological Network Construction, Path Mining and Visualization
netprioR	Fabian Schmich	A model for network-based prioritisation of genes
netresponse	Leo Lahti	Functional Network Analysis
NetSAM	Zhiao Shi	Network Seriation And Modularization
netSmooth	Jonathan Ronen	Network smoothing for scRNAseq
networkBMA	Ka Yee Yeung	Regression-based network inference using Bayesian Model Averaging
NeuCA	Hao Feng	NEUral network-based single-Cell Annotation tool
NewWave	Federico Agostinis	Negative binomial model for scRNA-seq
ngsReports	Steve Pederson	Load FastqQC reports and other NGS related files
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
NoRCE	Gulden Olgun	NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment
normalize450K	Jonathan Alexander Heiss	Preprocessing of Illumina Infinium 450K data
NormalyzerDE	Jakob Willforss	Evaluation of normalization methods and calculation of differential expression analysis statistics
NormqPCR	James Perkins	Functions for normalisation of RT-qPCR data
normr	Johannes Helmuth	Normalization and difference calling in ChIP-seq data
NPARC	Nils Kurzawa	Non-parametric analysis of response curves for thermal proteome profiling experiments
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	Alba Sala	Nucleosome positioning package for R
nuCpos	Hiroaki Kato	An R package for prediction of nucleosome positions
nullranges	Michael Love	Generation of null ranges via bootstrapping or covariate matching
NuPoP	Ji-Ping Wang	An R package for nucleosome positioning prediction
NxtIRFcore	Alex Chit Hei Wong	Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine
occugene	Oliver Will	Functions for Multinomial Occupancy Distribution
OCplus	Alexander Ploner	Operating characteristics plus sample size and local fdr for microarray experiments
ODER	David Zhang	Optimising the Definition of Expressed Regions
odseq	José Jiménez	Outlier detection in multiple sequence alignments
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	Xavier Escribà Montagut	Exposome and omic data associatin and integration analysis
OmicsLonDA	Ahmed A. Metwally	Omics Longitudinal Differential Analysis
OMICsPCA	Subhadeep Das	An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
omicsPrint	Davy Cats	Cross omic genetic fingerprinting
Omixer	Lucy Sinke	Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies
OmnipathR	Denes Turei	OmniPath web service client and more
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	Luca De Sano	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)
onlineFDR	David S. Robertson	Online error control
ontoProc	VJ Carey	processing of ontologies of anatomy, cell lines, and so on
openCyto	Mike Jiang,Jake Wagner	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
OpenStats	Hamed Haseli Mashhadi	A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association
oposSOM	Henry Loeffler-Wirth	Comprehensive analysis of transcriptome data
oppar	Soroor Hediyeh zadeh	Outlier profile and pathway analysis in R
oppti	Abdulkadir Elmas	Outlier Protein and Phosphosite Target Identifier
optimalFlow	Hristo Inouzhe	optimalFlow
OPWeight	Mohamad Hasan	Optimal p-value weighting with independent information
OrderedList	Claudio Lottaz	Similarities of Ordered Gene Lists
ORFhunteR	Vasily V. Grinev	Predict open reading frames in nucleotide sequences
ORFik	Haakon Tjeldnes	Open Reading Frames in Genomics
Organism.dplyr	Martin Morgan	dplyr-based Access to Bioconductor Annotation Resources
OrganismDbi	Bioconductor Package Maintainer	Software to enable the smooth interfacing of different database packages
orthogene	Brian Schilder	Interspecies gene mapping
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
OUTRIDER	Christian Mertes	OUTRIDER - OUTlier in RNA-Seq fInDER
OVESEG	Lulu Chen	OVESEG-test to detect tissue/cell-specific markers
PAA	Michael Turewicz, Martin Eisenacher	PAA (Protein Array Analyzer)
packFinder	Jack Gisby	de novo Annotation of Pack-TYPE Transposable Elements
padma	Andrea Rau	Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
PADOG	Adi L. Tarca	Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
pageRank	Hongxu Ding	Temporal and Multiplex PageRank for Gene Regulatory Network Analysis
PAIRADISE	Qiang Hu, Levon Demirdjian	PAIRADISE: Paired analysis of differential isoform expression
paircompviz	Michal Burda	Multiple comparison test visualization
pairkat	Cameron Severn	PaIRKAT
pandaR	Joseph N. Paulson, Dan Schlauch	PANDA Algorithm
panelcn.mops	Gundula Povysil	CNV detection tool for targeted NGS panel data
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
parglms	VJ Carey	support for parallelized estimation of GLMs/GEEs
parody	Vince Carey	Parametric And Resistant Outlier DYtection
PAST	Thrash Adam	Pathway Association Study Tool (PAST)
Path2PPI	Oliver Philipp	Prediction of pathway-related protein-protein interaction networks
pathifier	Assif Yitzhaky	Quantify deregulation of pathways in cancer
PathNet	Ludwig Geistlinger	An R package for pathway analysis using topological information
PathoStat	Solaiappan Manimaran, Yue Zhao	PathoStat Statistical Microbiome Analysis Package
pathRender	Vince Carey	Render molecular pathways
pathVar	Samuel Zimmerman	Methods to Find Pathways with Significantly Different Variability
pathview	Weijun Luo	a tool set for pathway based data integration and visualization
pathwayPCA	Gabriel Odom	Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
paxtoolsr	Augustin Luna	Access Pathways from Multiple Databases Through BioPAX and Pathway Commons
pcaExplorer	Federico Marini	Interactive Visualization of RNA-seq Data Using a Principal Components Approach
pcaMethods	Henning Redestig	A collection of PCA methods
PCAN	Matthew Page and Patrice Godard	Phenotype Consensus ANalysis (PCAN)
PCAtools	Kevin Blighe	PCAtools: Everything Principal Components Analysis
pcxn	Sokratis Kariotis	Exploring, analyzing and visualizing functions utilizing the pcxnData package
PDATK	Benjamin Haibe-Kains	Pancreatic Ductal Adenocarcinoma Tool-Kit
pdInfoBuilder	Benilton Carvalho	Platform Design Information Package Builder
PeacoQC	Annelies Emmaneel	Peak-based selection of high quality cytometry data
peakPantheR	Arnaud Wolfer	Peak Picking and Annotation of High Resolution Experiments
PECA	Tomi Suomi	Probe-level Expression Change Averaging
peco	Chiaowen Joyce Hsiao	A Supervised Approach for Predicting cell Cycle Progression using scRNA-seq data
pengls	Stijn Hawinkel	Fit Penalised Generalised Least Squares models
PepsNMR	Manon Martin	Pre-process 1H-NMR FID signals
pepStat	Gregory C Imholte	Statistical analysis of peptide microarrays
pepXMLTab	Xiaojing Wang	Parsing pepXML files and filter based on peptide FDR.
PERFect	Quy Cao	Permutation filtration for microbiome data
periodicDNA	Jacques Serizay	Set of tools to identify periodic occurrences of k-mers in DNA sequences
perturbatr	Simon Dirmeier	Statistical Analysis of High-Throughput Genetic Perturbation Screens
PFP	XC Zhang	Pathway Fingerprint Framework in R
pgca	Gabriela Cohen-Freue	PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data
phantasus	Alexey Sergushichev	Visual and interactive gene expression analysis
PharmacoGx	Benjamin Haibe-Kains	Analysis of Large-Scale Pharmacogenomic Data
phemd	William S Chen	Phenotypic EMD for comparison of single-cell samples
PhenoGeneRanker	Cagatay Dursun	PhenoGeneRanker: A gene and phenotype prioritization tool
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
PhIPData	Athena Chen	Container for PhIP-Seq Experiments
phosphonormalizer	Sohrab Saraei	Compensates for the bias introduced by median normalization in
PhosR	Taiyun Kim	A set of methods and tools for comprehensive analysis of phosphoproteomics data
PhyloProfile	Vinh Tran	PhyloProfile
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 Wigge	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
pipeComp	Pierre-Luc Germain	pipeComp pipeline benchmarking framework
pipeFrame	Zheng Wei	Pipeline framework for bioinformatics in R
pkgDepTools	Bioconductor Package Maintainer	Package Dependency Tools
planet	Victor Yuan	Placental DNA methylation analysis tools
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
PloGO2	Jemma Wu, Dana Pascovici	Plot Gene Ontology and KEGG pathway Annotation and Abundance
plotgardener	Nicole Kramer	Coordinate-Based Genomic Visualization Package for R
plotGrouper	John D. Gagnon	Shiny app GUI wrapper for ggplot with built-in statistical analysis
PLPE	Soo-heang Eo	Local Pooled Error Test for Differential Expression with Paired High-throughput Data
plyranges	Stuart Lee	A fluent interface for manipulating GenomicRanges
pmm	Anna Drewek	Parallel Mixed Model
pmp	Gavin Rhys Lloyd	Peak Matrix Processing and signal batch correction for metabolomics datasets
PoDCall	Hans Petter Brodal	Positive Droplet Calling for DNA Methylation Droplet Digital PCR
podkat	Ulrich Bodenhofer	Position-Dependent Kernel Association Test
pogos	VJ Carey	PharmacOGenomics Ontology Support
polyester	Jack Fu, Jeff Leek	Simulate RNA-seq reads
POMA	Pol Castellano-Escuder	User-friendly Workflow for Metabolomics and Proteomics Data Analysis
PoTRA	Margaret Linan	PoTRA: Pathways of Topological Rank Analysis
powerTCR	Hillary Koch	Model-Based Comparative Analysis of the TCR Repertoire
POWSC	Kenong Su	Simulation, power evaluation, and sample size recommendation for single cell RNA-seq
ppcseq	Stefano Mangiola	Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models
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
pram	Peng Liu	Pooling RNA-seq datasets for assembling transcript models
prebs	Karolis Uziela	Probe region expression estimation for RNA-seq data for improved microarray comparability
preciseTAD	Mikhail Dozmorov	preciseTAD: A machine learning framework for precise TAD boundary prediction
PrecisionTrialDrawer	Giorgio Melloni	A Tool to Analyze and Design NGS Based Custom Gene Panels
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
primirTSS	Pumin Li	Prediction of pri-miRNA Transcription Start Site
PrInCE	Michael Skinnider	Predicting Interactomes from Co-Elution
proActiv	Joseph Lee	Estimate Promoter Activity from RNA-Seq data
proBAMr	Xiaojing Wang	Generating SAM file for PSMs in shotgun proteomics data
proBatch	Chloe H. Lee	Tools for Diagnostics and Corrections of Batch Effects in Proteomics
PROcess	Xiaochun Li	Ciphergen SELDI-TOF Processing
procoil	Ulrich Bodenhofer	Prediction of Oligomerization of Coiled Coil Proteins
proDA	Constantin Ahlmann-Eltze	Differential Abundance Analysis of Label-Free Mass Spectrometry Data
proFIA	Alexis Delabriere	Preprocessing of FIA-HRMS data
profileplyr	Tom Carroll, Doug Barrows	Visualization and annotation of read signal over genomic ranges with profileplyr
profileScoreDist	Paal O. Westermark	Profile score distributions
progeny	Aurélien Dugourd	Pathway RespOnsive GENes for activity inference from gene expression
projectR	Genevieve Stein-O'Brien	Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering
pRoloc	Laurent Gatto	A unifying bioinformatics framework for spatial proteomics
pRolocGUI	Laurent Gatto	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
proteinProfiles	Julian Gehring	Protein Profiling
ProteoDisco	Job van Riet	Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences
ProteomicsAnnotationHubData	Laurent Gatto	Transform public proteomics data resources into Bioconductor Data Structures
ProteoMM	Yuliya V Karpievitch	Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform
ProtGenerics	Laurent Gatto	Generic infrastructure for Bioconductor mass spectrometry packages
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
ptairMS	camille Roquencourt	Pre-processing PTR-TOF-MS Data
PubScore	Tiago Lubiana	Automatic calculation of literature relevance of genes
pulsedSilac	Marc Pagès-Gallego	Analysis of pulsed-SILAC quantitative proteomics data
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	Diego Diez	PWM enrichment analysis
pwOmics	Maren Sitte	Pathway-based data integration of omics data
pwrEWAS	Stefan Graw	A user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)
qckitfastq	August Guang	FASTQ Quality Control
qcmetrics	Laurent Gatto	A Framework for Quality Control
QDNAseq	Daoud Sie	Quantitative DNA Sequencing for Chromosomal Aberrations
QFeatures	Laurent Gatto	Quantitative features for mass spectrometry data
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
qPLEXanalyzer	Ashley Sawle	Tools for qPLEX-RIME data analysis
qrqc	Vince Buffalo	Quick Read Quality Control
qsea	Matthias Lienhard	IP-seq data analysis and vizualization
qsmooth	Stephanie C. Hicks	Smooth quantile normalization
QSutils	Mercedes Guerrero-Murillo	Quasispecies Diversity
Qtlizer	Matthias Munz	Comprehensive QTL annotation of GWAS results
quantiseqr	Federico Marini	Quantification of the Tumor Immune contexture from RNA-seq data
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 or	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
RadioGx	Benjamin Haibe-Kains	Analysis of Large-Scale Radio-Genomic Data
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
ramr	Oleksii Nikolaienko	Detection of Rare Aberrantly Methylated Regions in Array and NGS Data
ramwas	Andrey A Shabalin	Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
RandomWalkRestartMH	Alberto Valdeolivas	Random walk with restart on multiplex and heterogeneous Networks
randPack	Robert Gentleman	Randomization routines for Clinical Trials
randRotation	Peter Hettegger	Random Rotation Methods for High Dimensional Data with Batch Structure
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
rawrr	Christian Panse	Direct Access to Orbitrap Data and Beyond
RbcBook1	Vince Carey	Support for Springer monograph on Bioconductor
Rbec	Pengfan Zhang	Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities
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, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
rCGH	Frederic Commo	Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
RcisTarget	Sara Aibar	RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions
RCM	Joris Meys	Fit row-column association models with the negative binomial distribution for the microbiome
Rcpi	Nan Xiao	Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
RCSL	Qinglin Mei	Rank Constrained Similarity Learning for single cell RNA sequencing data
Rcwl	Qiang Hu	An R interface to the Common Workflow Language
RcwlPipelines	Qiang Hu	Bioinformatics pipelines based on Rcwl
RCy3	Alex Pico	Functions to Access and Control Cytoscape
RCyjs	Paul Shannon	Display and manipulate graphs in cytoscape.js
rDGIdb	Lars Bosshard	R Wrapper for DGIdb
Rdisop	Steffen Neumann	Decomposition of Isotopic Patterns
RDRToolbox	Christoph Bartenhagen	A package for nonlinear dimension reduction with Isomap and LLE.
ReactomeContentService4R	Chi-Lam Poon	Interface for the Reactome Content Service
ReactomeGraph4R	Chi-Lam Poon	Interface for the Reactome Graph Database
ReactomeGSA	Johannes Griss	Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
ReactomePA	Guangchuang Yu	Reactome Pathway Analysis
ReadqPCR	James Perkins	Read qPCR data
REBET	Bill Wheeler	The subREgion-based BurdEn Test (REBET)
rebook	Aaron Lun	Re-using Content in Bioconductor Books
receptLoss	Daniel Pique	Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors
reconsi	Joris Meys	Resampling Collapsed Null Distributions for Simultaneous Inference
recount	Leonardo Collado-Torres	Explore and download data from the recount project
recount3	Leonardo Collado-Torres	Explore and download data from the recount3 project
recountmethylation	Sean K Maden	Access and analyze DNA methylation database compilations
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
RefPlus	Kai-Ming Chang	A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
RegEnrich	Weiyang Tao	Gene regulator enrichment analysis
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
regutools	Joselyn Chavez	regutools: an R package for data extraction from RegulonDB
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
RepViz	Thomas Faux, Asta Laiho	Replicate oriented Visualization of a genomic region
ReQON	Christopher Cabanski	Recalibrating Quality Of Nucleotides
ResidualMatrix	Aaron Lun	Creating a DelayedMatrix of Regression Residuals
restfulSE	Shweta Gopaulakrishnan	Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
rexposome	Xavier Escribà Montagut	Exposome exploration and outcome data analysis
rfaRm	Lara Selles Vidal, Rafael Ayala	An R interface to the Rfam database
Rfastp	Thomas Carroll	An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).
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
rGenomeTracks	Omar Elashkar	Integerated visualization of epigenomic data
Rgin	Hector Climente-Gonzalez	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	R Interface to HDF5
rhdf5client	Vincent Carey	Access HDF5 content from h5serv
rhdf5filters	Mike Smith	HDF5 Compression Filters
Rhdf5lib	Mike Smith	hdf5 library as an R package
Rhisat2	Charlotte Soneson	R Wrapper for HISAT2 Aligner
Rhtslib	Bioconductor Package Maintainer	HTSlib high-throughput sequencing library as an R package
RiboCrypt	Michal Swirski	Interactive visualization in genomics
RiboDiPA	Ji-Ping Wang	Differential pattern analysis for Ribo-seq data
RiboProfiling	A. Popa	Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
ribor	Michael Geng	An R Interface for Ribo Files
riboSeqR	Thomas J. Hardcastle	Analysis of sequencing data from ribosome profiling experiments
ribosomeProfilingQC	Jianhong Ou	Ribosome Profiling Quality Control
RImmPort	Zicheng Hu, Ravi Shankar	RImmPort: Enabling Ready-for-analysis Immunology Research Data
Ringo	J. Toedling	R Investigation of ChIP-chip Oligoarrays
RIPAT	Min-Jeong Baek	Retroviral Integration Pattern Analysis Tool (RIPAT)
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)
RLassoCox	Wei Liu	A reweighted Lasso-Cox by integrating gene interaction information
RLMM	Nusrat Rabbee	A Genotype Calling Algorithm for Affymetrix SNP Arrays
RLSeq	Henry Miller	RLSeq: An analysis package for R-loop mapping data
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
rmelting	J. Aravind	R Interface to MELTING 5
RmiR	Francesco Favero	Package to work with miRNAs and miRNA targets with R
Rmmquant	Zytnicki Matthias	RNA-Seq multi-mapping Reads Quantification Tool
rmspc	Meriem Bahda	Multiple Sample Peak Calling
RNAAgeCalc	Xu Ren	A multi-tissue transcriptional age calculator
RNAdecay	Reed Sorenson	Maximum Likelihood Decay Modeling of RNA Degradation Data
rnaEditr	Lanyu Zhang	Statistical analysis of RNA editing sites and hyper-editing regions
RNAinteract	Mike Smith	Estimate Pairwise Interactions from multidimensional features
RNAmodR	Felix G.M. Ernst	Detection of post-transcriptional modifications in high throughput sequencing data
RNAmodR.AlkAnilineSeq	Felix G.M. Ernst	Detection of m7G, m3C and D modification by AlkAnilineSeq
RNAmodR.ML	Felix G.M. Ernst	Detecting patterns of post-transcriptional modifications using machine learning
RNAmodR.RiboMethSeq	Felix G.M. Ernst	Detection of 2'-O methylations by RiboMethSeq
RNAsense	Marcus Rosenblatt	Analysis of Time-Resolved RNA-Seq Data
rnaseqcomp	Mingxiang Teng	Benchmarks for RNA-seq Quantification Pipelines
RNASeqPower	Terry M Therneau	Sample size for RNAseq studies
RNASeqR	Kuan-Hao Chao	RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RnaSeqSampleSize	Shilin Zhao Developer	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 microarray focus
ROCpAI	Juan-Pedro Garcia	Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers
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
ROSeq	Krishan Gupta	Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data
ROTS	Tomi Suomi	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
rrvgo	Sergi Sayols	Reduce + Visualize GO
Rsamtools	Bioconductor Package Maintainer	Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
rsbml	Michael Lawrence	R support for SBML, using libsbml
rScudo	Matteo Ciciani	Signature-based Clustering for Diagnostic Purposes
rsemmed	Leslie Myint	An interface to the Semantic MEDLINE database
RSeqAn	August Guang	R SeqAn
Rsubread	Wei Shi, Yang Liao and Gordon K Smyth	Mapping, quantification and variant analysis of sequencing data
RSVSim	Christoph Bartenhagen	RSVSim: an R/Bioconductor package for the simulation of structural variations
rSWeeP	Danrley R. Fernandes	Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
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	RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
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
Rtpca	Nils Kurzawa	Thermal proximity co-aggregation with R
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 Protein-Protein Interaction 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	rWikiPathways - R client library for the WikiPathways API
S4Vectors	Bioconductor Package Maintainer	Foundation of vector-like and list-like containers in Bioconductor
safe	Ludwig Geistlinger	Significance Analysis of Function and Expression
sagenhaft	Tim Beissbarth	Collection of functions for reading and comparing SAGE libraries
SAIGEgds	Xiuwen Zheng	Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies
sampleClassifier	Khadija El Amrani	Sample Classifier
SamSPECTRAL	Habil	Identifies cell population in flow cytometry data
sangeranalyseR	Kuan-Hao Chao	sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
sangerseqR	Jonathon Hill	Tools for Sanger Sequencing Data in R
SANTA	Alex Cornish	Spatial Analysis of Network Associations
sarks	Dennis Wylie	Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains
satuRn	Jeroen Gilis	Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
savR	R. Brent Calder	Parse and analyze Illumina SAV files
SBGNview	Weijun Luo	"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
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
ScaledMatrix	Aaron Lun	Creating a DelayedMatrix of Scaled and Centered Values
scAlign	Nelson Johansen	An alignment and integration method for single cell genomics
SCAN.UPC	Stephen R. Piccolo	Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
scanMiR	Fridolin Gross	scanMiR
scanMiRApp	Pierre-Luc Germain	scanMiR shiny application
scAnnotatR	Johannes Griss	Pretrained learning models for cell type prediction on single cell RNA-sequencing data
SCANVIS	Phaedra Agius	SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
SCArray	Xiuwen Zheng	Large-scale single-cell RNA-seq data manipulation with GDS files
SCATE	Wenpin Hou	SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement
scater	Alan O'Callaghan	Single-Cell Analysis Toolkit for Gene Expression Data in R
scatterHatch	Atul Deshpande	Creates hatched patterns for scatterplots
scBFA	Ruoxin Li	A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
SCBN	Yan Zhou	A statistical normalization method and differential expression analysis for RNA-seq data between different species
scCB2	Zijian Ni	CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
scClassifR	Johannes Griss	Pretrained learning models for cell type prediction on single cell RNA-sequencing data
scClassify	Yingxin Lin	scClassify: single-cell Hierarchical Classification
scDataviz	Kevin Blighe	scDataviz: single cell dataviz and downstream analyses
scDblFinder	Pierre-Luc Germain	scDblFinder
scDD	Keegan Korthauer	Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
scde	Jean Fan	Single Cell Differential Expression
scds	Dennis Kostka	In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
SCFA	Duc Tran	SCFA: Subtyping via Consensus Factor Analysis
scFeatureFilter	Guillaume Devailly	A correlation-based method for quality filtering of single-cell RNAseq data
scGPS	Quan Nguyen	A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)
schex	Saskia Freytag	Hexbin plots for single cell omics data
scHOT	Shila Ghazanfar	single-cell higher order testing
ScISI	Tony Chiang	In Silico Interactome
scMAGeCK	Xiaolong Cheng	Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data
scmap	Vladimir Kiselev	A tool for unsupervised projection of single cell RNA-seq data
scMerge	Yingxin Lin	scMerge: Merging multiple batches of scRNA-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	Davide Risso	Single Cell Overview of Normalized Expression data
Sconify	Tyler J Burns	A toolkit for performing KNN-based statistics for flow and mass cytometry data
SCOPE	Rujin Wang	A normalization and copy number estimation method for single-cell DNA sequencing
scoreInvHap	Dolors Pelegri-Siso	Get inversion status in predefined regions
scp	Christophe Vanderaa	Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
scPCA	Philippe Boileau	Sparse Contrastive Principal Component Analysis
scPipe	Luyi Tian	pipeline for single cell RNA-seq data analysis
scran	Aaron Lun	Methods for Single-Cell RNA-Seq Data Analysis
scReClassify	Taiyun Kim	scReClassify: post hoc cell type classification of single-cell RNA-seq data
scRecover	Zhun Miao	scRecover for imputation of single-cell RNA-seq data
scRepertoire	Nick Borcherding	A toolkit for single-cell immune receptor profiling
scruff	Zhe Wang	Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
scry	Kelly Street	Small-Count Analysis Methods for High-Dimensional Data
scShapes	Malindrie Dharmaratne	A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data
scTensor	Koki Tsuyuzaki	Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition
scTGIF	Koki Tsuyuzaki	Cell type annotation for unannotated single-cell RNA-Seq data
scTHI	Michele Ceccarelli	Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data
scTreeViz	Jayaram Kancherla	R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations
scuttle	Aaron Lun	Single-Cell RNA-Seq Analysis Utilities
SDAMS	Yuntong Li	Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data
sechm	Pierre-Luc Germain	sechm: Complex Heatmaps from a SummarizedExperiment
segmenter	Mahmoud Ahmed	Perform Chromatin Segmentation Analysis in R by Calling ChromHMM
segmentSeq	Thomas J. Hardcastle	Methods for identifying small RNA loci from high-throughput sequencing data
selectKSigs	Zhi Yang	Selecting the number of mutational signatures using a perplexity-based measure and cross-validation
SELEX	Harmen J. Bussemaker	Functions for analyzing SELEX-seq data
SemDist	Ian Gonzalez	Information Accretion-based Function Predictor Evaluation
semisup	Armin Rauschenberger	Semi-Supervised Mixture Model
SEPIRA	Yuting Chen	Systems EPigenomics Inference of Regulatory Activity
seq2pathway	Arjun Kinstlick	a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data
SeqArray	Xiuwen Zheng	Data management of large-scale 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
SeqGate	Stéphanie Rialle	Filtering of Lowly Expressed Features
SeqGSEA	Xi Wang	Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
seqLogo	Robert Ivanek	Sequence logos for DNA sequence alignments
seqPattern	Vanja Haberle	Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences
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
sesame	Wanding Zhou	SEnsible Step-wise Analysis of DNA MEthylation BeadChips
SEtools	Pierre-Luc Germain	SEtools: tools for working with SummarizedExperiment
sevenbridges	Soner Koc	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
SharedObject	Jiefei Wang	Sharing R objects across multiple R processes without memory duplication
shinyepico	Octavio Morante-Palacios	ShinyÉPICo
shinyMethyl	Jean-Philippe Fortin	Interactive visualization for Illumina methylation arrays
ShortRead	Bioconductor Package Maintainer	FASTQ input and manipulation
SIAMCAT	Jakob Wirbel	Statistical Inference of Associations between Microbial Communities And host phenoTypes
SICtools	Xiaobin Xing	Find SNV/Indel differences between two bam files with near relationship
SigCheck	Rory Stark	Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
sigFeature	Pijush Das Developer	sigFeature: Significant feature selection using SVM-RFE & t-statistic
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
signatureSearch	Yuzhu Duan	Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
signeR	Renan Valieris	Empirical Bayesian approach to mutational signature discovery
sigPathway	Weil Lai	Pathway Analysis
SigsPack	Franziska Schumann	Mutational Signature Estimation for Single Samples
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
SIMD	Jiadi Zhu	Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site
SimFFPE	Lanying Wei	NGS Read Simulator for FFPE Tissue
similaRpeak	Astrid Deschenes	Metrics to estimate a level of similarity between two ChIP-Seq profiles
SIMLR	Luca De Sano	Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)
simplifyEnrichment	Zuguang Gu	Simplify Functional Enrichment Results
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
SingleCellSignalR	Jacques Colinge	Cell Signalling Using Single Cell RNAseq Data Analysis
singleCellTK	Yichen Wang	Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
SingleMoleculeFootprinting	Guido Barzaghi	Analysis tools for Single Molecule Footprinting (SMF) data
SingleR	Aaron Lun	Reference-Based Single-Cell RNA-Seq Annotation
singscore	Dharmesh D. Bhuva	Rank-based single-sample gene set scoring method
SISPA	Bhakti Dwivedi	SISPA: Method for Sample Integrated Set Profile Analysis
sitadela	Panagiotis Moulos	An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms
sitePath	Chengyang Ji	Phylogeny-based sequence clustering with site polymorphism
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
slingshot	Kelly Street	Tools for ordering single-cell sequencing
slinky	Eric Kort	Putting the fun in LINCS L1000 data analysis
SLqPCR	Matthias Kohl	Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH
SMAD	Qingzhou Zhang	Statistical Modelling of AP-MS Data (SMAD)
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
snapcount	Rone Charles	R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
snifter	Alan O'Callaghan	R wrapper for the python openTSNE library
snm	John D. Storey	Supervised Normalization of Microarrays
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
sojourner	Sojourner Developer	Statistical analysis of single molecule trajectories
SomaticSignatures	Julian Gehring	Somatic Signatures
SOMNiBUS	Kathleen Klein	Smooth modeling of bisulfite sequencing
SpacePAC	Gregory Ryslik	Identification of Mutational Clusters in 3D Protein Space via Simulation.
Spaniel	Rachel Queen	Spatial Transcriptomics Analysis
sparrow	Steve Lianoglou	Take command of set enrichment analyses through a unified interface
sparseDOSSA	Boyu Ren, Emma Schwager, George Weingart	Sparse Data Observations for Simulating Synthetic Abundance
sparseMatrixStats	Constantin Ahlmann-Eltze	Summary Statistics for Rows and Columns of Sparse Matrices
sparsenetgls	Irene Zeng	Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression
SparseSignatures	Luca De Sano	SparseSignatures
SpatialCPie	Joseph Bergenstraahle	Cluster analysis of Spatial Transcriptomics data
spatialDE	Davide Corso	R wrapper for SpatialDE
SpatialDecon	Nicole Ortogero	Deconvolution of mixed cells from spatial and/or bulk gene expression data
SpatialExperiment	Dario Righelli	S4 Class for Spatial Experiments handling
spatialHeatmap	Jianhai Zhang	spatialHeatmap
spatzie	Jennifer Hammelman	Identification of enriched motif pairs from chromatin interaction data
specL	Christian Panse	specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
SpeCond	Florence Cavalli	Condition specific detection from expression data
Spectra	RforMassSpectrometry Package Maintainer	Spectra Infrastructure for Mass Spectrometry Data
SpectralTAD	Kellen Cresswell	SpectralTAD: Hierarchical TAD detection using spectral clustering
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
spicyR	Ellis Patrick	Spatial analysis of in situ cytometry data
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
spiky	Tim Triche	Spike-in calibration for cell-free MeDIP
spkTools	Matthew N McCall	Methods for Spike-in Arrays
splatter	Luke Zappia	Simple Simulation of Single-cell RNA Sequencing Data
SplicingFactory	Endre Sebestyen	Splicing Diversity Analysis for Transcriptome Data
SplicingGraphs	H. Pagès	Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
splineTimeR	Herbert Braselmann, Martin Selmansberger	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
spqn	Yi Wang	Spatial quantile normalization
SPsimSeq	Joris Meys	Semi-parametric simulation tool for bulk and single-cell RNA sequencing data
SQLDataFrame	Qian Liu	Representation of SQL database in DataFrame metaphor
SQUADD	Martial Sankar	Add-on of the SQUAD Software
sRACIPE	Vivek Kohar	Systems biology tool to simulate gene regulatory circuits
SRAdb	Jack Zhu	A compilation of metadata from NCBI SRA and tools
SRGnet	Isar Nassiri	SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data
srnadiff	Zytnicki Matthias	Finding differentially expressed unannotated genomic regions from RNA-seq data
sscore	Richard Kennedy	S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
sscu	Yu Sun	Strength of Selected Codon Usage
sSeq	Danni Yu	Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
ssize	Gregory R. Warnes	Estimate Microarray Sample Size
ssPATHS	Natalie R. Davidson	ssPATHS: Single Sample PATHway Score
ssrch	VJ Carey	a simple search engine
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
STATegRa	David Gomez-Cabrero, Núria Planell	Classes and methods for multi-omics data integration
statTarget	Hemi Luan	Statistical Analysis of Molecular Profiles
stepNorm	Yuanyuan Xiao	Stepwise normalization functions for cDNA microarrays
strandCheckR	Thu-Hien To	Calculate strandness information of a bam file
Streamer	Martin Morgan	Enabling stream processing of large files
STRINGdb	Damian Szklarczyk	STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis
STROMA4	Sadiq Saleh	Assign Properties to TNBC Patients
struct	Gavin Rhys Lloyd	Statistics in R Using Class-based Templates
Structstrings	Felix G.M. Ernst	Implementation of the dot bracket annotations with Biostrings
structToolbox	Gavin Rhys Lloyd	Data processing & analysis tools for Metabolomics and other omics
StructuralVariantAnnotation	Daniel Cameron	Variant annotations for structural variants
SubCellBarCode	Taner Arslan	SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome
subSeq	Andrew J. Bass, John D. Storey	Subsampling of high-throughput sequencing count data
SummarizedBenchmark	Patrick Kimes	Classes and methods for performing benchmark comparisons
SummarizedExperiment	Bioconductor Package Maintainer	SummarizedExperiment container
Summix	Audrey Hendricks	Summix: A method to estimate and adjust for population structure in genetic summary data
supersigs	Albert Kuo	Supervised mutational signatures
supraHex	Hai Fang	supraHex: a supra-hexagonal map for analysing tabular omics data
surfaltr	Pooja Gangras	Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr
survcomp	Benjamin Haibe-Kains	Performance Assessment and Comparison for Survival Analysis
survtype	Dongmin Jung	Subtype Identification with Survival Data
Sushi	Douglas H Phanstiel	Tools for visualizing genomics data
sva	Jeffrey T. Leek, John D. Storey, W. Evan Johnson	Surrogate Variable Analysis
svaNUMT	Ruining Dong	NUMT detection from structural variant calls
svaRetro	Ruining Dong	Retrotransposed transcript detection from structural variants
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	Estimation of the science-wise false discovery rate and the false discovery rate conditional on covariates
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
synapsis	Lucy McNeill	An R package to automate the analysis of double-strand break repair during meiosis
synapter	Laurent Gatto Sebastian Gibb	Label-free data analysis pipeline for optimal identification and quantitation
synergyfinder	Shuyu Zheng	Calculate and Visualize Synergy Scores for Drug Combinations
SynExtend	Nicholas Cooley	Tools for Working With Synteny Objects
synlet	Chunxuan Shao	Hits Selection for Synthetic Lethal RNAi Screen Data
SynMut	Haogao Gu	SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures
systemPipeR	Thomas Girke	systemPipeR: NGS workflow and report generation environment
systemPipeShiny	Le Zhang	systemPipeShiny: An Interactive Framework for Workflow Management and Visualization
systemPipeTools	Daniela Cassol	Tools for data visualization
TADCompare	Kellen Cresswell	TADCompare: Identification and characterization of differential TADs
tanggle	Klaus Schliep	Visualization of Phylogenetic Networks
TAPseq	Andreas R. Gschwind	Targeted scRNA-seq primer design for TAP-seq
target	Mahmoud Ahmed	Predict Combined Function of Transcription Factors
TargetDecoy	Elke Debrie	Diagnostic Plots to Evaluate the Target Decoy Approach
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
TBSignatureProfiler	Aubrey Odom	Profile RNA-Seq Data Using TB Pathway Signatures
TCC	Jianqiang Sun, Tomoaki Nishiyama	TCC: Differential expression analysis for tag count data with robust normalization strategies
TCGAbiolinks	Tiago Chedraoui Silva, Antonio Colaprico	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	Sarah Bonnin	Quality control for target capture experiments
ternarynet	McCall N. Matthew	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	Vincent Carey	TFutils
tidybulk	Stefano Mangiola	Brings transcriptomics to the tidyverse
tidySingleCellExperiment	Stefano Mangiola	Brings SingleCellExperiment to the Tidyverse
tidySummarizedExperiment	Stefano Mangiola	Brings SummarizedExperiment to the Tidyverse
tigre	Antti Honkela	Transcription factor Inference through Gaussian process Reconstruction of Expression
TileDBArray	Aaron Lun	Using TileDB as a DelayedArray Backend
tilingArray	Zhenyu Xu	Transcript mapping with high-density oligonucleotide tiling arrays
timecourse	Yu Chuan Tai	Statistical Analysis for Developmental Microarray Time Course Data
timeOmics	Antoine Bodein	Time-Course Multi-Omics data integration
timescape	Maia Smith	Patient Clonal Timescapes
TimeSeriesExperiment	Lan Huong Nguyen	Analysis for short time-series data
TimiRGeN	Krutik Patel	Time sensitive microRNA-mRNA integration, analysis and network generation tool
TIN	Bjarne Johannessen	Transcriptome instability analysis
TissueEnrich	Ashish Jain	Tissue-specific gene enrichment analysis
TitanCNA	Gavin Ha	Subclonal copy number and LOH prediction from whole genome sequencing of tumours
tkWidgets	J. Zhang	R based tk widgets
tLOH	Michelle Webb	Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations
TMixClust	Monica Golumbeanu	Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines
TNBC.CMS	Doyeong Yu	TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes
TnT	Jialin Ma	Interactive Visualization for Genomic Features
TOAST	Ziyi Li	Tools for the analysis of heterogeneous tissues
tofsims	Lorenz Gerber	Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
tomoda	Wendao Liu	Tomo-seq data analysis
topconfects	Paul Harrison	Top Confident Effect Sizes
topdownr	Sebastian Gibb	Investigation of Fragmentation Conditions in Top-Down Proteomics
topGO	Adrian Alexa	Enrichment Analysis for Gene Ontology
ToxicoGx	Benjamin Haibe-Kains	Analysis of Large-Scale Toxico-Genomic Data
TPP	Dorothee Childs	Analyze thermal proteome profiling (TPP) experiments
TPP2D	Nils Kurzawa	Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)
tracktables	Tom Carroll	Build IGV tracks and HTML reports
trackViewer	Jianhong Ou	A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data
tradeSeq	Hector Roux de Bezieux	trajectory-based differential expression analysis for sequencing data
TrajectoryGeometry	Michael Shapiro	This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns
TrajectoryUtils	Aaron Lun	Single-Cell Trajectory Analysis Utilities
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
transformGamPoi	Constantin Ahlmann-Eltze	Variance Stabilizing Transformation for Gamma-Poisson Models
transite	Konstantin Krismer	RNA-binding protein motif analysis
tRanslatome	Toma Tebaldi, Erik Dassi	Comparison between multiple levels of gene expression
transomics2cytoscape	Kozo Nishida	A tool set for 3D Trans-Omic network visualization with Cytoscape
TransView	Julius Muller	Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
TraRe	Jesus De La Fuente Cedeño	Transcriptional Rewiring
traseR	li chen	GWAS trait-associated SNP enrichment analyses in genomic intervals
Travel	Jiefei Wang	An utility to create an ALTREP object with a virtual pointer
traviz	Koen Van den Berge	Trajectory functions for visualization and interpretation.
TreeAndLeaf	Milena A. Cardoso	Displaying binary trees with focus on dendrogram leaves
treeio	Guangchuang Yu	Base Classes and Functions for Phylogenetic Tree Input and Output
treekoR	Adam Chan	Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations
TreeSummarizedExperiment	Ruizhu Huang	TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
trena	Paul Shannon	Fit transcriptional regulatory networks using gene expression, priors, machine learning
Trendy	Rhonda Bacher	Breakpoint analysis of time-course expression data
TRESS	Zhenxing Guo	Toolbox for mRNA epigenetics sequencing analysis
tricycle	Shijie Zheng	tricycle: Transferable Representation and Inference of cell cycle
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
tripr	Iason Ofeidis	T-cell Receptor/Immunoglobulin Profiler (TRIP)
tRNA	Felix GM Ernst	Analyzing tRNA sequences and structures
tRNAdbImport	Felix G.M. Ernst	Importing from tRNAdb and mitotRNAdb as GRanges objects
tRNAscanImport	Felix G.M. Ernst	Importing a tRNAscan-SE result file as GRanges object
TRONCO	Luca De Sano	TRONCO, an R package for TRanslational ONCOlogy
TSCAN	Zhicheng Ji	Tools for Single-Cell Analysis
tscR	Fernando Pérez-Sanz	A time series clustering package combining slope and Frechet distances
tspair	Jeffrey T. Leek	Top Scoring Pairs for Microarray Classification
TSRchitect	R. Taylor Raborn	Promoter identification from large-scale TSS profiling data
ttgsea	Dongmin Jung	Tokenizing Text of Gene Set Enrichment Analysis
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
txcutr	Mervin Fansler	Transcriptome CUTteR
tximeta	Michael Love	Transcript Quantification Import with Automatic Metadata
tximport	Michael Love	Import and summarize transcript-level estimates for transcript- and gene-level analysis
TypeInfo	Duncan Temple Lang	Optional Type Specification Prototype
Ularcirc	David Humphreys	Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
UMI4Cats	Mireia Ramos-Rodriguez	UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
uncoverappLib	Emanuela Iovino	Interactive graphical application for clinical assessment of sequence coverage at the base-pair level
UNDO	Niya Wang	Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions
unifiedWMWqPCR	Joris Meys	Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
UniProt.ws	Bioconductor Package Maintainer	R Interface to UniProt Web Services
Uniquorn	'Raik Otto'	Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
universalmotif	Benjamin Jean-Marie Tremblay	Import, Modify, and Export Motifs with R
uSORT	Hao Chen	uSORT: A self-refining ordering pipeline for gene selection
VAExprs	Dongmin Jung	Generating Samples of Gene Expression Data with Variational Autoencoders
VanillaICE	R.B. Scharpf	A Hidden Markov Model for high throughput genotyping arrays
VarCon	Johannes Ptok	VarCon: an R package for retrieving neighboring nucleotides of an SNV
variancePartition	Gabriel E. Hoffman	Quantify and interpret divers of variation in multilevel gene expression experiments
VariantAnnotation	Bioconductor Package Maintainer	Annotation of Genetic Variants
VariantExperiment	Qian Liu	A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
VariantFiltering	Robert Castelo	Filtering of coding and non-coding genetic variants
VariantTools	Michael Lawrence	Tools for Exploratory Analysis of Variant Calls
VaSP	Huihui Yu	Quantification and Visualization of Variations of Splicing in Population
vbmp	Nicola Lama	Variational Bayesian Multinomial Probit Regression
VCFArray	Qian Liu	Representing on-disk / remote VCF files as array-like objects
VegaMC	Sandro Morganella	VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer
velociraptor	Kevin Rue-Albrecht	Toolkit for Single-Cell Velocity
veloviz	Lyla Atta	VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories
VennDetail	Kai Guo	A package for visualization and extract details
VERSO	Davide Maspero	Viral Evolution ReconStructiOn (VERSO)
vidger	Brandon Monier	Create rapid visualizations of RNAseq data in R
viper	Mariano J Alvarez	Virtual Inference of Protein-activity by Enriched Regulon analysis
ViSEAGO	Aurelien Brionne	ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
vissE	Dharmesh D. Bhuva	Visualising Set Enrichment Analysis Results
VplotR	Jacques Serizay	Set of tools to make V-plots and compute footprint profiles
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
waddR	Julian Flesch	Statistical tests for detecting differential distributions based on the 2-Wasserstein distance
wateRmelon	Leo C Schalkwyk	Illumina 450 and EPIC methylation array normalization and metrics
wavClusteR	Federico Comoglio	Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
weaver	Seth Falcon	Tools and extensions for processing Sweave documents
webbioc	Colin A. Smith	Bioconductor Web Interface
weitrix	Paul Harrison	Tools for matrices with precision weights, test and explore weighted or sparse data
widgetTools	Jianhua Zhang	Creates an interactive tcltk widget
wiggleplotr	Kaur Alasoo	Make read coverage plots from BigWig files
wpm	Helene Borges	Well Plate Maker
wppi	Ana Galhoz	Weighting protein-protein interactions
Wrench	Hector Corrada Bravo	Wrench normalization for sparse count data
XCIR	Renan Sauteraud	XCI-inference
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
Xeva	Benjamin Haibe-Kains	Analysis of patient-derived xenograft (PDX) data
XINA	Lang Ho Lee and Sasha A. Singh	Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis
xmapbridge	Chris Wirth	Export plotting files to the xmapBridge for visualisation in X:Map
XNAString	Marianna Plucinska	Efficient Manipulation of Modified Oligonucleotide Sequences
XVector	Hervé Pagès	Foundation of external vector representation and manipulation in Bioconductor
yamss	Leslie Myint	Tools for high-throughput metabolomics
YAPSA	Daniel Huebschmann	Yet Another Package for Signature Analysis
yarn	Joseph N Paulson	YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
zellkonverter	Luke Zappia	Conversion Between scRNA-seq Objects
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