Bioconductor Software Packages

Bioconductor version: 3.13

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
AffyExpress Xuejun Arthur Li Affymetrix Quality Assessment and Analysis Tool
affyILM Myriam Kroll and Fabrice Berger Linear Model of background subtraction and the Langmuir isotherm
affyio Ben Bolstad Tools for parsing Affymetrix data files
affylmGUI Gordon Smyth GUI for limma Package with Affymetrix Microarrays
affyPara Markus Schmidberger Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays
affyPLM Ben Bolstad Methods for fitting probe-level models
affyQCReport Craig Parman QC Report Generation for affyBatch objects
AffyRNADegradation Mario Fasold Analyze and correct probe positional bias in microarray data due to RNA degradation
AGDEX Cuilan lani Gao Agreement of Differential Expression Analysis
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 Luis Fernandez 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
AnnotationFuncs Stefan McKinnon Edwards Annotation translation functions
AnnotationHub Bioconductor Package Maintainer Client to access AnnotationHub resources
AnnotationHubData Bioconductor Package Maintainer Transform public data resources into Bioconductor Data Structures
annotationTools Alexandre Kuhn Annotate microarrays and perform cross-species gene expression analyses using flat file databases
annotatr Raymond G. Cavalcante Annotation of Genomic Regions to Genomic Annotations
anota Ola Larsson ANalysis Of Translational Activity (ANOTA).
anota2seq Christian Oertlin, Julie Lorent Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
antiProfiles Hector Corrada Bravo Implementation of gene expression anti-profiles
AnVIL Martin Morgan Bioconductor on the AnVIL compute environment
AnVILBilling Vince Carey Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (
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
ArrayTools Arthur Li geneChip Analysis Package
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
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
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
bigmemoryExtras Peter M. Haverty An extension of the bigmemory package with added safety, convenience, and a factor class
bigPint Lindsay Rutter Big multivariate data plotted interactively
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
BiocCaseStudies Bioconductor Package Maintainer BiocCaseStudies: Support for the Case Studies Monograph
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
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
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
BUMHMM Alina Selega Computational pipeline for computing probability of modification from structure probing experiment data
bumphunter Rafael A. Irizarry 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
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
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
CancerMutationAnalysis Simina M. Boca Cancer mutation analysis
CancerSubtypes Taosheng Xu Cancer subtypes identification, validation and visualization based on multiple genomic data sets
CAnD Caitlin McHugh Perform Chromosomal Ancestry Differences (CAnD) Analyses
caOmicsV Henry Zhang Visualization of multi-dimentional cancer genomics data
Cardinal Kylie A. Bemis A mass spectrometry imaging toolbox for statistical analysis
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
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)
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
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
CGEN Nilotpal Sanyal 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
ChIPSeqSpike Nicolas Descostes ChIP-Seq data scaling according to spike-in control
ChIPsim Peter Humburg Simulation of ChIP-seq experiments
ChIPXpress George Wu ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
chopsticks Hin-Tak Leung The 'snp.matrix' and 'X.snp.matrix' Classes
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
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 Enio Gjerga 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
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
CompGO Ashley J. Waardenberg An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
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
CoRegFlux Pauline Trébulle and Mohamed Elati CoRegFlux
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
CrossICC Yu Sun An Interactive Consensus Clustering Framework for Multi-platform Data Analysis
crossmeta Alex Pickering Cross Platform Meta-Analysis of Microarray Data
CSAR Jose M Muino Statistical tools for the analysis of ChIP-seq data
csaw Aaron Lun ChIP-Seq Analysis with Windows
CSSP Chandler Zuo ChIP-Seq Statistical Power
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
cytofast K.A. Stam cytofast - A quick visualization and analysis tool for CyTOF data
CytoGLMM Christof Seiler Conditional Differential Analysis for Flow and Mass Cytometry Experiments
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
DBChIP Kun Liang Differential Binding of Transcription Factor with ChIP-seq
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
decoupleR Jesús Vélez Package to decouple gene sets from statistics
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
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
dexus Guenter Klambauer DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
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
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 Aaron Lun 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
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
EasyqpcR Le Pape Sylvain EasyqpcR for low-throughput real-time quantitative PCR data analysis
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
EDDA Chia Kuan Hui Burton, Niranjan Nagarajan Experimental Design in Differential Abundance analysis
edge John D. Storey, Andrew J. Bass Extraction of Differential Gene Expression
edgeR Yunshun Chen, 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
eisa Gabor Csardi Expression data analysis via the Iterative Signature Algorithm
eisaR Michael Stadler Exon-Intron Split Analysis (EISA) in R
ELBOW Graham Alvare, Xiangli Zhang ELBOW - Evaluating foLd change By the lOgit Way
ELMER Tiago Chedraoui Silva Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
EMDomics Sadhika Malladi and Daniel Schmolze Earth Mover's Distance for Differential Analysis of Genomics Data
EmpiricalBrownsMethod David Gibbs Uses Brown's method to combine p-values from dependent tests
ENCODExplorer Charles Joly Beauparlant A compilation of ENCODE metadata
EnhancedVolcano Kevin Blighe Publication-ready volcano plots with enhanced colouring and labeling
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
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 Suhaib Mohammed Download datasets from EMBL-EBI Expression Atlas
ExpressionView Gabor Csardi Visualize biclusters identified in gene expression data
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
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
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
FlowRepositoryR Josef Spidlen FlowRepository R Interface
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 Produces Summaries and Plots of Features Distributed Across Genomes
GenomicFeatures Bioconductor Package Maintainer Conveniently import and query gene models
GenomicFiles Bioconductor Package Maintainer Distributed computing by file or by range
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
genoset Peter M. Haverty A RangedSummarizedExperiment with methods for copy number analysis
genotypeeval Jennifer Tom QA/QC of a gVCF or VCF file
genphen Simo Kitanovski A tool for quantification of associations between genotypes and phenotypes in genome wide association studies (GWAS) with Bayesian inference and statistical learning
GenVisR Zachary Skidmore Genomic Visualizations in R
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
GGPA Dongjun Chung graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
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 Maya McDaniel Exploring the Human Cell Atlas Data Coordinating Platform
HCABrowser Bioconductor Package Maintainer Browse the Human Cell Atlas data portal
HCAExplorer Bioconductor Package Maintainer Browse the Human Cell Atlas data portal
HCAMatrixBrowser Marcel Ramos Extract and manage matrix data from the Human Cell Atlas project
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
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
Imetagene Audrey Lemacon A graphical interface for the metagene package
IMMAN Minoo Ashtiani Interlog protein network reconstruction by Mapping and Mining ANalysis
ImmuneSpaceR ImmuneSpace Package Maintainer A Thin Wrapper around the ImmuneSpace Database
immunoClust Till Soerensen immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
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 Shawn Balcome Package for enabling powerful shiny web displays of Bioconductor objects
interactiveDisplayBase Shawn Balcome Base package for enabling powerful shiny web displays of Bioconductor objects
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
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
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 James Collins, Henry Holm, Daniel Lowenstein 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
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
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 Pan Du Mass spectrum processing by wavelet-based algorithms
MAST Andrew McDavid Model-based Analysis of Single Cell Transcriptomics
matchBox Luigi Marchionni, Anuj Gupta Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.
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 Ariane Schad 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
mdgsa David Montaner Multi Dimensional Gene Set Analysis.
mdp Helder Nakaya Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
mdqc Gabriela Cohen-Freue Mahalanobis Distance Quality Control for microarrays
MDTS Jack M.. Fu Detection of de novo deletion in targeted sequencing trios
MEAL 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
metagenomeFeatures Nathan D. Olson Exploration of marker-gene sequence taxonomic annotations
metagenomeSeq Joseph N. Paulson Statistical analysis for sparse high-throughput sequencing
metahdep John R. Stevens Hierarchical Dependence in Meta-Analysis
metaMS 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
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
methyAnalysis Lei Huang DNA methylation data analysis and visualization
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
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
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
MicrobiotaProcess Shuangbin Xu an R package for analysis, visualization and biomarker discovery of microbiome
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
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
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)
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
MsCoreUtils RforMassSpectrometry Package Maintainer Core Utils for Mass Spectrometry Data
MSEADbi Kozo Nishida DBI to construct MSEA-related package
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
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 The package maintainer 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 Rurika Oka 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 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 nanotatoR: next generation structural variant annotation and classification
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
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
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
NuPoP Ji-Ping Wang An R package for nucleosome positioning prediction
occugene Oliver Will Functions for Multinomial Occupancy Distribution
OCplus Alexander Ploner Operating characteristics plus sample size and local fdr for microarray experiments
odseq José Jiménez Outlier detection in multiple sequence alignments
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 Randomize Samples for -omics Profiling
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
OSAT Li Yan OSAT: Optimal Sample Assignment Tool
Oscope Ning Leng Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
OTUbase Daniel Beck Provides structure and functions for the analysis of OTU data
OutlierD Sukwoo Kim Outlier detection using quantile regression on the M-A scatterplots of high-throughput data
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
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 PaxtoolsR: 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
pcot2 Sarah Song Principal Coordinates and Hotelling's T-Square method
PCpheno Nolwenn Le Meur Phenotypes and cellular organizational units
pcxn Sokratis Kariotis Exploring, analyzing and visualizing functions utilizing the pcxnData package
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 **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
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
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
Polyfit Conrad Burden Add-on to DESeq to improve p-values and q-values
POMA Pol Castellano-Escuder User-friendly Workflow for Metabolomics and Proteomics Data Analysis
POST Xueyuan Cao Projection onto Orthogonal Space Testing for High Dimensional Data
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 Spiro Stilianoudakis 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 Alberto Valdeolivas 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
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 Urbelz 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
RchyOptimyx Adrin Jalali, Nima Aghaeepour Optimyzed Cellular Hierarchies for Flow Cytometry
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
RDAVIDWebService Cristobal Fresno An R Package for retrieving data from DAVID into R objects using Web Services API.
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
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
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
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
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
RNAither Lars Kaderali Statistical analysis of high-throughput RNAi screens
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
RNAprobR Nikos Sidiropoulos An R package for analysis of massive parallel sequencing based RNA structure probing data
RNAsense Marcus Rosenblatt Analysis of Time-Resolved RNA-Seq Data
rnaseqcomp Mingxiang Teng Benchmarks for RNA-seq Quantification Pipelines
rnaSeqMap Michal Okoniewski rnaSeq secondary analyses
RNASeqPower Terry M Therneau Sample size for RNAseq studies
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 PPI networks
rTRMui Diego Diez A shiny user interface for rTRM
runibic Patryk Orzechowski runibic: row-based biclustering algorithm for analysis of gene expression data in R
RUVcorr Saskia Freytag Removal of unwanted variation for gene-gene correlations and related analysis
RUVnormalize Laurent Jacob RUV for normalization of expression array data
RUVSeq Davide Risso Remove Unwanted Variation from RNA-Seq Data
RVS Thomas Sherman Computes estimates of the probability of related individuals sharing a rare variant
rWikiPathways Egon Willighagen 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
SAGx Per Broberg, Statistical Analysis of the GeneChip
SAIGEgds Xiuwen Zheng Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies
samExploreR shailesh tripathi samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
sampleClassifier Khadija El Amrani Sample Classifier
SamSPECTRAL Habil 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)
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
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
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
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
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
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
seqplots Przemyslaw Stempor An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
seqsetvis Joseph R Boyd Set Based Visualizations for Next-Gen Sequencing Data
SeqSQC Qian Liu A bioconductor package for sample quality check with next generation sequencing data
seqTools Wolfgang Kaisers Analysis of nucleotide, sequence and quality content on fastq files
SeqVarTools Stephanie M. Gogarten Tools for variant data
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
simulatorZ Yuqing Zhang Simulator for Collections of Independent Genomic Data Sets
sincell Miguel Julia, Antonio Rausell R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
SingleCellExperiment Davide Risso S4 Classes for Single Cell Data
SingleCellSignalR Jacques Colinge Cell Signalling Using Single Cell RNAseq Data Analysis
singleCellTK Yusuke Koga 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 Phylogenetic pathway–dependent recognition of fixed substitutions and parallel mutations
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 J. 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
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
SpatialDecon Patrick Danaher 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
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
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
SSPA Maarten van Iterson General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data
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 (Search Tool for the Retrieval of Interacting proteins database)
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
survcomp Benjamin Haibe-Kains, Markus Schroeder, Catharina Olsen 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
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
synapter Laurent Gatto and 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
TAPseq Andreas Gschwind Targeted scRNA-seq primer design for TAP-seq
target Mahmoud Ahmed Predict Combined Function of Transcription Factors
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
ToPASeq Ivana Ihnatova Topology-based pathway analysis of RNA-seq data
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
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
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 Proportions to Parent
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
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
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 Pérez-Sanz, Fernando 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
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 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
VanillaICE Robert 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
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 Illumina 450 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
XBSeq Yuanhang Liu Test for differential expression for RNA-seq 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
yaqcaffy Laurent Gatto Affymetrix expression data quality control and reproducibility 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

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