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Bioconductor Software Packages

Bioconductor version: Release (3.19)

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
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
adverSCarial Ghislain FIEVET adverSCarial, generate and analyze the vulnerability of scRNA-seq classifiers to adversarial attacks
AffiXcan Alessandro Lussana A Functional Approach To Impute Genetically Regulated Expression
affxparser Kasper Daniel Hansen Affymetrix File Parsing SDK
affy Robert D. Shear Methods for Affymetrix Oligonucleotide Arrays
affycomp Robert D. Shear Graphics Toolbox for Assessment of Affymetrix Expression Measures
affyContam V. Carey structured corruption of affymetrix cel file data
affycoretools James W. MacDonald Functions useful for those doing repetitive analyses with Affymetrix GeneChips
affyILM Myriam Kroll and Fabrice Berger Linear Model of background subtraction and the Langmuir isotherm
affyio Ben Bolstad Tools for parsing Affymetrix data files
affylmGUI Gordon Smyth GUI for limma Package with Affymetrix Microarrays
affyPLM Ben Bolstad Methods for fitting probe-level models
AffyRNADegradation Mario Fasold Analyze and correct probe positional bias in microarray data due to RNA degradation
AGDEX Cuilan lani Gao Agreement of Differential Expression Analysis
aggregateBioVar Jason Ratcliff Differential Gene Expression Analysis for Multi-subject scRNA-seq
agilp Benny Chain Agilent expression array processing package
AgiMicroRna Pedro Lopez-Romero Processing and Differential Expression Analysis of Agilent microRNA chips
AHMassBank Johannes Rainer MassBank Annotation Resources for AnnotationHub
AIMS Eric R Paquet AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
airpart Wancen Mu Differential cell-type-specific allelic imbalance
alabaster Aaron Lun Umbrella for the Alabaster Framework
alabaster.base Aaron Lun Save Bioconductor Objects To File
alabaster.bumpy Aaron Lun Save and Load BumpyMatrices to/from file
alabaster.files Aaron Lun Wrappers to Save Common File Formats
alabaster.mae Aaron Lun Load and Save MultiAssayExperiments
alabaster.matrix Aaron Lun Load and Save Artifacts from File
alabaster.ranges Aaron Lun Load and Save Ranges-related Artifacts from File
alabaster.sce Aaron Lun Load and Save SingleCellExperiment from File
alabaster.schemas Aaron Lun Schemas for the Alabaster Framework Aaron Lun Load and Save SummarizedExperiments from File
alabaster.spatial Aaron Lun Save and Load Spatial 'Omics Data to/from File
alabaster.string Aaron Lun Save and Load Biostrings to/from File
alabaster.vcf Aaron Lun Save and Load Variant Data to/from File
ALDEx2 Greg Gloor Analysis Of Differential Abundance Taking Sample and Scale 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
AlphaMissenseR Martin Morgan Accessing AlphaMissense Data Resources in R
AlpsNMR Sergio Oller Moreno Automated spectraL Processing System for NMR
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 Microbiome differential abudance and correlation analyses 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 Jessica McClintock Interactive microbiome analysis toolkit
annaffy Colin A. Smith Annotation tools for Affymetrix biological metadata
annmap Chris Wirth Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
annotate Bioconductor Package Maintainer Annotation for microarrays
AnnotationDbi Bioconductor Package Maintainer Manipulation of SQLite-based annotations in Bioconductor
AnnotationFilter Bioconductor Package Maintainer Facilities for Filtering Bioconductor Annotation Resources
AnnotationForge Bioconductor Package Maintainer Tools for building SQLite-based annotation data packages
AnnotationHub Bioconductor Package Maintainer Client to access AnnotationHub resources
AnnotationHubData Bioconductor Package Maintainer Transform public data resources into Bioconductor Data Structures
annotationTools Alexandre Kuhn Annotate microarrays and perform cross-species gene expression analyses using flat file databases
annotatr Raymond G. Cavalcante Annotation of Genomic Regions to Genomic Annotations
anota Ola Larsson ANalysis Of Translational Activity (ANOTA).
anota2seq Christian Oertlin, Ola Larsson Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
antiProfiles Hector Corrada Bravo Implementation of gene expression anti-profiles
AnVIL Marcel Ramos Bioconductor on the AnVIL compute environment
AnVILBilling Vince Carey Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (
AnVILPublish Marcel Ramos Publish Packages and Other Resources to AnVIL Workspaces
AnVILWorkflow Sehyun Oh Run workflows implemented in Terra/AnVIL workspace
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
APL Clemens Kohl Association Plots
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 Jose Marugan Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
arrayMvout V. Carey multivariate outlier detection for expression array QA
arrayQuality Agnes Paquet Assessing array quality on spotted arrays
arrayQualityMetrics Mike Smith Quality metrics report for microarray data sets
ARRmNormalization Jean-Philippe Fortin Adaptive Robust Regression normalization for Illumina methylation data
artMS David Jimenez-Morales Analytical R tools for Mass Spectrometry
ASAFE Qian Zhang Ancestry Specific Allele Frequency Estimation
ASEB Likun Wang Predict Acetylated Lysine Sites
ASGSCA Hela Romdhani Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models
ASICS Gaëlle Lefort Automatic Statistical Identification in Complex Spectra
ASpli Ariel Chernomoretz 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)
ASURAT Keita Iida Functional annotation-driven unsupervised clustering for single-cell data
ATACCoGAPS Rossin Erbe Analysis Tools for scATACseq Data with CoGAPS
ATACseqQC Jianhong Ou ATAC-seq Quality Control
ATACseqTFEA Jianhong Ou Transcription Factor Enrichment Analysis for ATAC-seq
atena Robert Castelo Analysis of Transposable Elements
atSNP Sunyoung Shin Affinity test for identifying regulatory SNPs
attract Samuel Zimmerman Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
AUCell Gert Hulselmans AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
autonomics Aditya Bhagwat Unified statistal Modeling of Omics Data
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
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 Context-Aware Transcript Quantification from Long Read RNA-Seq data
bamsignals Johannes Helmuth Extract read count signals from bam files
BANDITS Simone Tiberi BANDITS: Bayesian ANalysis of DIfferenTial Splicing
bandle Oliver M. Crook An R package for the Bayesian analysis of differential subcellular localisation experiments
Banksy Joseph Lee Spatial transcriptomic clustering
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 Catalina Vallejos Bayesian Analysis of Single-Cell Sequencing data
BASiCStan Alan O'Callaghan Stan implementation of BASiCS
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 Jessica McClintock 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 Samuel Granjeaud 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
beachmat.hdf5 Aaron Lun beachmat bindings for HDF5-backed matrices
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 Livia Rasp Correction of batch effects in DNA methylation data
beer Athena Chen Bayesian Enrichment Estimation in R
benchdamic Matteo Calgaro Benchmark of differential abundance methods on microbiome data
BERT Yannis Schumann Hierarchical Batch-Effect Adjustment with Trees
betaHMM Koyel Majumdar A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data
bettr Charlotte Soneson A Better Way To Explore What Is Best
BG2 Jacob Williams Performs Bayesian GWAS analysis for non-Gaussian data using BG2
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
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 Leonard C. Schalkwyk Illumina methylation array analysis for large experiments
BindingSiteFinder Mirko Brüggemann Binding site defintion based on iCLIP data
bioassayR Daniela Cassol Cross-target analysis of small molecule bioactivity
Biobase Bioconductor Package Maintainer Biobase: Base functions for Bioconductor
biobroom John D. Storey and Andrew J. Bass Turn Bioconductor objects into tidy data frames
biobtreeR Tamer Gur Using biobtree tool from R
bioCancer Karim Mezhoud Interactive Multi-Omics Cancers Data Visualization and Analysis
BioCartaImage Zuguang Gu BioCarta Pathway Images
BiocBaseUtils Marcel Ramos General utility functions for developing Bioconductor packages
BiocBook Jacques Serizay Write, containerize, publish and version Quarto books with Bioconductor
BiocCheck Marcel Ramos Bioconductor-specific package checks
BiocFHIR Vincent Carey Illustration of FHIR ingestion and transformation using R
BiocFileCache Lori Shepherd Manage Files Across Sessions
BiocGenerics Hervé Pagès S4 generic functions used in Bioconductor
biocGraph Florian Hahne Graph examples and use cases in Bioinformatics
BiocHail Vincent Carey basilisk and hail
BiocHubsShiny Marcel Ramos View AnnotationHub and ExperimentHub Resources Interactively
BiocIO Marcel Ramos 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 Martin Morgan Bioconductor facilities for parallel evaluation
BiocPkgTools Sean Davis Collection of simple tools for learning about Bioconductor Packages
biocroxytest Francesc Catala-Moll Handle Long Tests in Bioconductor Packages
BiocSet Kayla Morrell Representing Different Biological Sets
BiocSingular Aaron Lun Singular Value Decomposition for Bioconductor Packages
BiocSklearn Vince Carey interface to python sklearn via Rstudio reticulate
BiocStyle Bioconductor Package Standard styles for vignettes and other Bioconductor documents
biocthis Leonardo Collado-Torres Automate package and project setup for Bioconductor packages
BiocVersion Bioconductor Package Maintainer Set the appropriate version of Bioconductor packages
biocViews Bioconductor Package Maintainer Categorized views of R package repositories
BiocWorkflowTools Mike Smith Tools to aid the development of Bioconductor Workflow packages
biodb Pierrick Roger biodb, a library and a development framework for connecting to chemical and biological databases
biodbChebi Pierrick Roger biodbChebi, a library for connecting to the ChEBI Database
biodbExpasy Pierrick Roger biodbExpasy, a library for connecting to Expasy ENZYME database.
biodbHmdb Pierrick Roger biodbHmdb, a library for connecting to the HMDB Database
biodbKegg Pierrick Roger biodbKegg, a library for connecting to the KEGG Database
biodbLipidmaps Pierrick Roger biodbLipidmaps, a library for connecting to the Lipidmaps Structure database
biodbNcbi Pierrick Roger biodbNcbi, a library for connecting to NCBI Databases.
biodbNci Pierrick Roger biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database
biodbUniprot Pierrick Roger biodbUniprot, a library for connecting to the Uniprot Database
bioDist Bioconductor Package Maintainer Different distance measures
biomaRt Mike Smith Interface to BioMart databases (i.e. Ensembl)
biomformat Paul J. McMurdie An interface package for the BIOM file format
BioMVCClass Elizabeth Whalen Model-View-Controller (MVC) Classes That Use Biobase
biomvRCNS Yang Du Copy Number study and Segmentation for multivariate biological data
BioNAR Anatoly Sorokin Biological Network Analysis in R
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 Etienne A. Thevenot Signature discovery from omics data
Biostrings Hervé 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
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 Van-Dung Pham 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
BOBaFIT Gaia Mazzocchetti Refitting diploid region profiles using a clustering procedure
borealis Garrett Jenkinson Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution
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
branchpointer Beth Signal Prediction of intronic splicing branchpoints
breakpointR David Porubsky Find breakpoints in Strand-seq data
brendaDb Yi Zhou The BRENDA Enzyme Database
BREW3R.r Lucille Lopez-Delisle R package associated to BREW3R
BRGenomics Mike DeBerardine Tools for the Efficient Analysis of High-Resolution Genomics Data
BridgeDbR Egon Willighagen Code for using BridgeDb identifier mapping framework from within R
BrowserViz Arkadiusz Gladki BrowserViz: interactive R/browser graphics using websockets and JSON
BSgenome Hervé Pagès Software infrastructure for efficient representation of full genomes and their SNPs
BSgenomeForge Hervé Pagès Forge BSgenome data packages
bsseq Kasper Daniel Hansen Analyze, manage and store bisulfite sequencing data
BubbleTree Todd Creasy, Wei Zhu BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
BufferedMatrix Ben Bolstad A matrix data storage object held in temporary files
BufferedMatrixMethods Ben Bolstad Microarray Data related methods that utlize BufferedMatrix objects
bugsigdbr Ludwig Geistlinger R-side access to published microbial signatures from BugSigDB
BUMHMM Alina Selega Computational pipeline for computing probability of modification from structure probing experiment data
bumphunter Tamilselvi Guharaj Bump Hunter
BumpyMatrix Aaron Lun Bumpy Matrix of Non-Scalar Objects
BUS Yuanhua Liu Gene network reconstruction
BUScorrect Xiangyu Luo Batch Effects Correction with Unknown Subtypes
BUSpaRse Lambda Moses kallisto | bustools R utilities
BUSseq Fangda Song Batch Effect Correction with Unknow Subtypes for scRNA-seq data
CaDrA Reina Chau Candidate Driver Analysis
CAEN Zhou Yan Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
CAFE Sander Bollen Chromosmal Aberrations Finder in Expression data
CAGEfightR Malte Thodberg Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
cageminer Fabrício Almeida-Silva Candidate Gene Miner
CAGEr Charles Plessy Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
calm Kun Liang Covariate Assisted Large-scale Multiple testing
CAMERA Steffen Neumann Collection of annotation related methods for mass spectrometry data
CaMutQC Xin Wang An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations
canceR Karim Mezhoud A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC
cancerclass Daniel Kosztyla Development and validation of diagnostic tests from high-dimensional molecular data
CancerInSilico Thomas D. Sherman, Elana J. Fertig An R interface for computational modeling of tumor progression
CancerSubtypes Taosheng Xu Cancer subtypes identification, validation and visualization based on multiple genomic data sets
cardelino Davis McCarthy Clone Identification from Single Cell Data
Cardinal Kylie Ariel Bemis A mass spectrometry imaging toolbox for statistical analysis
CardinalIO Kylie Ariel Bemis Read and write mass spectrometry imaging files
CARNIVAL Attila Gabor 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
CBEA Quang Nguyen Competitive Balances for Taxonomic Enrichment Analysis in R
cBioPortalData Marcel Ramos Exposes and Makes Available Data from the cBioPortal Web Resources
CBNplot Noriaki Sato plot bayesian network inferred from gene expression data based on enrichment analysis results
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
ccImpute Marcin Malec ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (
ccmap Alex Pickering Combination Connectivity Mapping
CCPlotR Sarah Ennis Plots For Visualising Cell-Cell Interactions
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
CDI Jiyuan Fang Clustering Deviation Index (CDI)
celaref Sarah Williams Single-cell RNAseq cell cluster labelling by reference
celda Joshua Campbell CEllular Latent Dirichlet Allocation
CellaRepertorium Andrew McDavid Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
CellBarcode Wenjie Sun Cellular DNA Barcode Analysis toolkit
cellbaseR Mohammed OE Abdallah Querying annotation data from the high performance Cellbase web
CellBench Shian Su Construct Benchmarks for Single Cell Analysis Methods
cellHTS2 Wolfgang Huber 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 Attila Gabor Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
cellscape Shixiang Wang 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
cellxgenedp Martin Morgan Discover and Access Single Cell Data Sets in the CELLxGENE Data Portal
CEMiTool Helder Nakaya Co-expression Modules identification Tool
censcyt Reto Gerber Differential abundance analysis with a right censored covariate in high-dimensional cytometry
Cepo Hani Jieun Kim Cepo for the identification of differentially stable genes
ceRNAnetsim Selcen Ari Yuka Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)
CeTF Carlos Alberto Oliveira de Biagi Junior Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
CexoR Pedro Madrigal An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
CFAssay Herbert Braselmann Statistical analysis for the Colony Formation Assay
cfdnakit Pitithat Puranachot Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)
cfDNAPro Haichao Wang cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA
cfTools Ran Hu Informatics Tools for Cell-Free DNA Study
CGEN Justin Lee An R package for analysis of case-control studies in genetic epidemiology
CGHbase Mark van de Wiel CGHbase: Base functions and classes for arrayCGH data analysis.
CGHcall Mark van de Wiel Calling aberrations for array CGH tumor profiles.
cghMCR J. Zhang Find chromosome regions showing common gains/losses
CGHnormaliter Bart P.P. van Houte Normalization of array CGH data with imbalanced aberrations.
CGHregions Sjoerd Vosse Dimension Reduction for Array CGH Data with Minimal Information Loss.
ChAMP Yuan Tian Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
ChemmineOB Thomas Girke R interface to a subset of OpenBabel functionalities
ChemmineR Thomas Girke Cheminformatics Toolkit for R
CHETAH Jurrian de Kanter Fast and accurate scRNA-seq cell type identification
Chicago Mikhail Spivakov CHiCAGO: Capture Hi-C Analysis of Genomic Organization
chihaya Aaron Lun Save Delayed Operations to a HDF5 File
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 Kai Wang Gene Set Enrichment For ChIP-seq Peak Data
ChIPexoQual Rene Welch ChIPexoQual
ChIPpeakAnno Jianhong Ou, Lihua Julie Zhu, Kai Hu, Junhui Li Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data
ChIPQC Tom Carroll, Rory Stark Quality metrics for ChIPseq data
ChIPseeker Guangchuang Yu ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
chipseq Bioconductor Package Maintainer chipseq: A package for analyzing chipseq data
ChIPseqR Peter Humburg Identifying Protein Binding Sites in High-Throughput Sequencing Data
ChIPsim Peter Humburg Simulation of ChIP-seq experiments
ChIPXpress George Wu ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
chopsticks Hin-Tak Leung The 'snp.matrix' and 'X.snp.matrix' Classes
chromDraw Jan Janecka chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.
ChromHeatMap Tim F. Rayner Heat map plotting by genome coordinate
chromPlot Karen Y. Orostica Global visualization tool of genomic data
ChromSCape Pacome Prompsy Analysis of single-cell epigenomics datasets with a Shiny App
chromstaR Aaron Taudt Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
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 Predict 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
CircSeqAlignTk Jianqiang Sun A toolkit for end-to-end analysis of RNA-seq data for circular genomes
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
clevRvis Sarah Sandmann Visualization Techniques for Clonal Evolution
clippda Stephen Nyangoma A package for the clinical proteomic profiling data analysis
clipper Paolo Martini Gene Set Analysis Exploiting Pathway Topology
cliProfiler You Zhou A package for the CLIP data visualization
cliqueMS Oriol Senan Campos Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
Clomial Habil Zare Infers clonal composition of a tumor
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
ClustAll Asier Ortega-Legarreta ClustAll: Data driven strategy to find groups of patients within complex diseases
clustComp Aurora Torrente Clustering Comparison Package
clusterExperiment Elizabeth Purdom Compare Clusterings for Single-Cell Sequencing
ClusterFoldSimilarity Oscar Gonzalez-Velasco Calculate similarity of clusters from different single cell samples using foldchanges
ClusterJudge Adrian Pasculescu Judging Quality of Clustering Methods using Mutual Information
clusterProfiler Guangchuang Yu A universal enrichment tool for interpreting omics data
clusterSeq Samuel Granjeaud 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 Kent Riemondy Classifier for Single-cell RNA-seq Using Cell Clusters
ClustIRR Simo Kitanovski Clustering of immune receptor repertoires
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 Attila Gabor Integration of CellNOptR to add missing links
CNORfuzzy T. Cokelaer Addon to CellNOptR: Fuzzy Logic
CNORode Attila Gabor ODE add-on to CellNOptR
CNTools J. Zhang Convert segment data into a region by sample matrix to allow for other high level computational analyses.
CNVfilteR Jose Marcos Moreno-Cabrera Identifies false positives of CNV calling tools by using SNV calls
CNVgears Simone Montalbano A Framework of Functions to Combine, Analize and Interpret CNVs Calling Results
cnvGSA Joseph Lugo Gene Set Analysis of (Rare) Copy Number Variants
CNViz Rebecca Greenblatt Copy Number Visualization
CNVMetrics Astrid Deschênes Copy Number Variant Metrics
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
CoGAPS Elana J. Fertig, Thomas D. Sherman, Jeanette Johnson, Dmitrijs Lvovs Coordinated Gene Activity in Pattern Sets
cogena Zhilong Jia co-expressed gene-set enrichment analysis
cogeqc Fabrício Almeida-Silva Systematic quality checks on comparative genomics analyses
Cogito Annika Bürger Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets
coGPS Yingying Wei cancer outlier Gene Profile Sets
cola Zuguang Gu A Framework for Consensus Partitioning
comapr Ruqian Lyu Crossover analysis and genetic map construction
combi Stijn Hawinkel Compositional omics model based visual integration
coMET Tiphaine Martin coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
coMethDMR Fernanda Veitzman Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies
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 Mattia Furlan Tools for computational epigenomics
ComplexHeatmap Zuguang Gu Make Complex Heatmaps
CompoundDb Johannes Rainer Creating and Using (Chemical) Compound Annotation Databases
ComPrAn Petra Palenikova Complexome Profiling Analysis package
compSPOT Sydney Grant compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots
concordexR Kayla Jackson Calculate the concordex coefficient
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 Deschênes Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
consICA Petr V. Nazarov consensus Independent Component Analysis
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.
CopyNumberPlots Bernat Gel Create Copy-Number Plots using karyoploteR functionality
coRdon Anamaria Elek Codon Usage Analysis and Prediction of Gene Expressivity
CoRegNet Remy Nicolle CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoreGx Benjamin Haibe-Kains Classes and Functions to Serve as the Basis for Other 'Gx' Packages
Cormotif Yingying Wei Correlation Motif Fit
corral Lauren Hsu Correspondence Analysis for Single Cell Data
CORREP Dongxiao Zhu Multivariate Correlation Estimator and Statistical Inference Procedures.
coseq Andrea Rau Co-Expression Analysis of Sequencing Data
CoSIA Amanda D. Clark An Investigation Across Different Species and Tissues
cosmiq David Fischer cosmiq - COmbining Single Masses Into Quantities
cosmosR Attila Gabor COSMOS (Causal Oriented Search of Multi-Omic Space)
COSNet Marco Frasca Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings
COTAN Galfrè Silvia Giulia COexpression Tables ANalysis
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
CRISPRball Jared Andrews Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering
crisprBase Jean-Philippe Fortin Base functions and classes for CRISPR gRNA design
crisprBowtie Jean-Philippe Fortin Bowtie-based alignment of CRISPR gRNA spacer sequences
crisprBwa Jean-Philippe Fortin BWA-based alignment of CRISPR gRNA spacer sequences
crisprDesign Jean-Philippe Fortin Comprehensive design of CRISPR gRNAs for nucleases and base editors
crisprScore Jean-Philippe Fortin On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs
CRISPRseek Lihua Julie Zhu Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
crisprseekplus Alper Kucukural crisprseekplus
crisprShiny Jean-Philippe Fortin Exploring curated CRISPR gRNAs via Shiny
CrispRVariants Helen Lindsay Tools for counting and visualising mutations in a target location
crisprVerse Jean-Philippe Fortin Easily install and load the crisprVerse ecosystem for CRISPR gRNA design
crisprViz Jean-Philippe Fortin Visualization Functions for CRISPR gRNAs
crlmm Benilton S Carvalho, Robert Scharpf, Matt Ritchie Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
crossmeta Alex Pickering Cross Platform Meta-Analysis of Microarray Data
CSAR Jose M Muino Statistical tools for the analysis of ChIP-seq data
csaw Aaron Lun ChIP-Seq Analysis with Windows
csdR Jakob Peder Pettersen Differential gene co-expression
CSSQ Fan Lab at Georgia Institute of Technology Chip-seq Signal Quantifier Pipeline
ctc Antoine Lucas Cluster and Tree Conversion.
CTdata Laurent Gatto Data companion to CTexploreR
CTDquerier Xavier Escribà-Montagut Package for CTDbase data query, visualization and downstream analysis
CTexploreR Axelle Loriot Explores Cancer Testis Genes
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
CTSV Jinge Yu Developer Identification of cell-type-specific spatially variable genes accounting for excess zeros
cummeRbund Loyal A. Goff Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
CuratedAtlasQueryR Stefano Mangiola Queries the Human Cell Atlas
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
cypress Shilin Yu Cell-Type-Specific Power Assessment
CytoDx Zicheng Hu Robust prediction of clinical outcomes using cytometry data without cell gating
CyTOFpower Anne-Maud Ferreira Power analysis for CyTOF experiments
cytofQC Jill Lundell Labels normalized cells for CyTOF data and assigns probabilities for each label
CytoGLMM Christof Seiler Conditional Differential Analysis for Flow and Mass Cytometry Experiments
cytoKernel Tusharkanti Ghosh Differential expression using kernel-based score test
cytolib Mike Jiang C++ infrastructure for representing and interacting with the gated cytometry data
cytomapper Lasse Meyer Visualization of highly multiplexed imaging data in R
CytoMDS Philippe Hauchamps Low Dimensions projection of cytometry samples
cytoMEM Jonathan Irish Marker Enrichment Modeling (MEM)
CytoML Mike Jiang A GatingML Interface for Cross Platform Cytometry Data Sharing
CytoPipeline Philippe Hauchamps Automation and visualization of flow cytometry data analysis pipelines
CytoPipelineGUI Philippe Hauchamps GUI's for visualization of flow cytometry data analysis pipelines
cytoviewer Lasse Meyer An interactive multi-channel image viewer for R
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
Damsel Caitlin Page Damsel: an end to end analysis of DamID
DAPAR Samuel Wieczorek Tools for the Differential Analysis of Proteins Abundance with R
dar Francesc Catala-Moll Differential Abundance Analysis by Consensus
DART Charles Shijie Zheng Denoising Algorithm based on Relevance network Topology
dcanr Dharmesh D. Bhuva Differential co-expression/association network analysis
DCATS Xinyi Lin Differential Composition Analysis Transformed by a Similarity matrix
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
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
decontX Yuan Yin Decontamination of single cell genomics data
deconvR Irem B. Gündüz Simulation and Deconvolution of Omic Profiles
decoupleR Pau Badia-i-Mompel decoupleR: Ensemble of computational methods to infer biological activities from omics data
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
DegCre Brian S. Roberts Probabilistic association of DEGs to CREs from differential data
DegNorm Ji-Ping Wang DegNorm: degradation normalization for RNA-seq data
DEGraph Laurent Jacob Two-sample tests on a graph
DEGreport Lorena Pantano Report of DEG analysis
DEGseq Likun Wang Identify Differentially Expressed Genes from RNA-seq data
DelayedArray Hervé Pagès A unified framework for working transparently with on-disk and in-memory array-like datasets
DelayedDataFrame Qian Liu Delayed operation on DataFrame using standard DataFrame metaphor
DelayedMatrixStats Peter Hickey Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
DelayedRandomArray Aaron Lun Delayed Arrays of Random Values
DelayedTensor Koki Tsuyuzaki R package for sparse and out-of-core arithmetic and decomposition of Tensor
DELocal Rishi Das Roy Identifies differentially expressed genes with respect to other local genes
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 Shuai Guo Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
demuxmix Hans-Ulrich Klein Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models
demuxSNP Michael Lynch scRNAseq demultiplexing using cell hashing and SNPs
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
DepInfeR Junyan Lu Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling
DeProViR Matineh Rahmatbakhsh A Deep-Learning Framework Based on Pre-trained Sequence Embeddings for Predicting Host-Viral Protein-Protein Interactions
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
DESpace Peiying Cai DESpace: a framework to discover spatially variable genes
destiny Philipp Angerer Creates diffusion maps
DEsubs Aristidis G. Vrahatis, Panos Balomenos DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
DEWSeq bioinformatics team Hentze Differential Expressed Windows Based on Negative Binomial Distribution
DExMA Juan Antonio Villatoro-García Differential Expression Meta-Analysis
DEXSeq Alejandro Reyes Inference of differential exon usage in RNA-Seq
DFP Rodrigo Alvarez-Glez Gene Selection
DIAlignR Shubham Gupta Dynamic Programming Based Alignment of MS2 Chromatograms
DiffBind Rory Stark Differential Binding Analysis of ChIP-Seq Peak Data
diffcoexp Wenbin Wei Differential Co-expression Analysis
diffcyt Lukas M. Weber Differential discovery in high-dimensional cytometry via high-resolution clustering
DifferentialRegulation Simone Tiberi Differentially regulated genes from scRNA-seq data
diffGeneAnalysis Choudary Jagarlamudi Performs differential gene expression Analysis
diffHic Aaron Lun, Gordon Smyth, Hannah Coughlin Differential Analysis of Hi-C Data
DiffLogo Hendrik Treutler DiffLogo: A comparative visualisation of biooligomer motifs
diffuStats Sergio Picart-Armada Diffusion scores on biological networks
diffUTR Pierre-Luc Germain diffUTR: Streamlining differential exon and 3' UTR usage
diggit Mariano J Alvarez Inference of Genetic Variants Driving Cellular Phenotypes
Dino Jared Brown Normalization of Single-Cell mRNA Sequencing Data
dinoR Michaela Schwaiger Differential NOMe-seq analysis
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 McGrath Max 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
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
DNAfusion Christoffer Trier Maansson Identification of gene fusions using paired-end sequencing
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
doubletrouble Fabrício Almeida-Silva Identification and classification of duplicated genes
dpeak Dongjun Chung dPeak (Deconvolution of Peaks in ChIP-seq Analysis)
drawProteins Paul Brennan Package to Draw Protein Schematics from Uniprot API output
dreamlet Gabriel Hoffman Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs
DRIMSeq Malgorzata Nowicka Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
DriverNet Jiarui Ding Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer
DropletUtils Jonathan Griffiths Utilities for Handling Single-Cell Droplet Data
drugTargetInteractions Thomas Girke Drug-Target Interactions
DrugVsDisease j. Saez-Rodriguez Comparison of disease and drug profiles using Gene set Enrichment Analysis
DSS Hao Wu, Hao Feng Dispersion shrinkage for sequencing data
dStruct Krishna Choudhary Identifying differentially reactive regions from RNA structurome profiling data
DTA Bjoern Schwalb Dynamic Transcriptome Analysis
Dune Hector Roux de Bezieux Improving replicability in single-cell RNA-Seq cell type discovery
dupRadar Sergi Sayols, Holger Klein Assessment of duplication rates in RNA-Seq datasets
dyebias Philip Lijnzaad The GASSCO method for correcting for slide-dependent gene-specific dye bias
DynDoc Bioconductor Package Maintainer Dynamic document tools
easier Oscar Lapuente-Santana Estimate Systems Immune Response from RNA-seq data
EasyCellType Ruoxing Li Annotate cell types for scRNA-seq data
easylift Abdullah Al Nahid An R package to perform genomic liftover
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 Xiuyu Ma An R package for gene and isoform differential expression analysis of RNA-seq data
EBSeqHMM Ning Leng Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
ecolitk Laurent Gautier Meta-data and tools for E. coli
EDASeq Davide Risso Exploratory Data Analysis and Normalization for RNA-Seq
edge John D. Storey, Andrew J. Bass Extraction of Differential Gene Expression
edgeR Yunshun Chen, Gordon Smyth, Aaron Lun, Mark Robinson Empirical Analysis of Digital Gene Expression Data in R
EDIRquery Laura D.T. Vo Ngoc Query the EDIR Database For Specific Gene
eds Avi Srivastava eds: Low-level reader for Alevin EDS format
eegc Xiaoyuan Zhou Engineering Evaluation by Gene Categorization (eegc)
EGAD Sara Ballouz Extending guilt by association by degree
EGSEA Monther Alhamdoosh Ensemble of Gene Set Enrichment Analyses
eiR Thomas Girke Accelerated similarity searching of small molecules
eisaR Michael Stadler Exon-Intron Split Analysis (EISA) in R
ELMER Tiago Chedraoui Silva Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
EMDomics Sadhika Malladi and Daniel Schmolze Earth Mover's Distance for Differential Analysis of Genomics Data
EmpiricalBrownsMethod David Gibbs Uses Brown's method to combine p-values from dependent tests
EnhancedVolcano Kevin Blighe Publication-ready volcano plots with enhanced colouring and labeling
enhancerHomologSearch Jianhong Ou Identification of putative mammalian orthologs to given enhancer
EnMCB Xin Yu Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models
ENmix Zongli Xu Quality control and analysis tools for Illumina DNA methylation BeadChip
EnrichedHeatmap Zuguang Gu Making Enriched Heatmaps
EnrichmentBrowser Ludwig Geistlinger Seamless navigation through combined results of set-based and network-based enrichment analysis
enrichplot Guangchuang Yu Visualization of Functional Enrichment Result
enrichTF Zheng Wei Transcription Factors Enrichment Analysis
enrichViewNet Astrid Deschênes From functional enrichment results to biological networks
ensembldb Johannes Rainer Utilities to create and use Ensembl-based annotation databases
ensemblVEP Bioconductor Package Maintainer R Interface to Ensembl Variant Effect Predictor
epialleleR Oleksii Nikolaienko Fast, Epiallele-Aware Methylation Caller and Reporter
EpiCompare Thomas Roberts Comparison, Benchmarking & QC of Epigenomic Datasets
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
EpiMix Yuanning Zheng EpiMix: an integrative tool for the population-level analysis of DNA methylation
epimutacions Dolors Pelegri-Siso Robust outlier identification for DNA methylation data
epiNEM Martin Pirkl epiNEM
epiregulon Xiaosai Yao Gene regulatory network inference from single cell epigenomic data
epiregulon.extra Xiaosai Yao Companion package to epiregulon with additional plotting, differential and graph functions
epistack DEVAILLY Guillaume Heatmaps of Stack Profiles from Epigenetic Signals
epistasisGA Michael Nodzenski An R package to identify multi-snp effects in nuclear family studies using the GADGETS method
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
escheR Boyi Guo Unified multi-dimensional visualizations with Gestalt principles
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
exomePeak2 Zhen Wei Peak Calling and differential analysis for MeRIP-Seq
ExperimentHub Bioconductor Package Maintainer Client to access ExperimentHub resources
ExperimentHubData Bioconductor Package Maintainer Add resources to ExperimentHub
ExperimentSubset Irzam Sarfraz Manages subsets of data with Bioconductor Experiment objects
ExploreModelMatrix Charlotte Soneson Graphical Exploration of Design Matrices
ExpressionAtlas Pedro Madrigal Download datasets from EMBL-EBI Expression Atlas
extraChIPs Stevie Pederson Additional functions for working with ChIP-Seq data
fabia Andreas Mitterecker FABIA: Factor Analysis for Bicluster Acquisition
factDesign Denise Scholtens Factorial designed microarray experiment analysis
factR Fursham Hamid Functional Annotation of Custom Transcriptomes
faers Yun Peng R interface for FDA Adverse Event Reporting System
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
fastreeR Anestis Gkanogiannis Phylogenetic, Distance and Other Calculations on VCF and Fasta Files
fastseg Alexander Blume 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
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
FeatSeekR Tuemay Capraz FeatSeekR an R package for unsupervised feature selection
fedup Catherine Ross Fisher's Test for Enrichment and Depletion of User-Defined Pathways
FELLA Sergio Picart-Armada Interpretation and enrichment for metabolomics data
fenr Marek Gierlinski Fast functional enrichment for interactive applications
ffpe Levi Waldron Quality assessment and control for FFPE microarray expression data
fgga Flavio Spetale 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
findIPs Shuo Wang Influential Points Detection for Feature Rankings
FindIT2 Guandong Shang find influential TF and Target based on multi-omics data
FISHalyseR Karesh Arunakirinathan, Andreas Heindl FISHalyseR a package for automated FISH quantification
fishpond Michael Love Fishpond: downstream methods and tools for expression data
FitHiC Ruyu Tan Confidence estimation for intra-chromosomal contact maps
flagme Mark Robinson, Riccardo Romoli Analysis of Metabolomics GC/MS Data
FLAMES Changqing Wang FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
flowAI Gianni Monaco Automatic and interactive quality control for flow cytometry data
flowBeads Nikolas Pontikos flowBeads: Analysis of flow bead data
flowBin Kieran O'Neill Combining multitube flow cytometry data by binning
flowcatchR Federico Marini Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
flowCHIC Author: Joachim Schumann Analyze flow cytometric data using histogram information
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 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, Wade Rogers Fingerprinting for Flow Cytometry
flowGate Andrew Wight Interactive Cytometry Gating in R
flowGraph Alice Yue Identifying differential cell populations in flow cytometry data accounting for marker frequency
flowMap Chiaowen Joyce Hsiao Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test
flowMatch Ariful Azad Matching and meta-clustering in flow cytometry
flowMeans Nima Aghaeepour Non-parametric Flow Cytometry Data Gating
flowMerge Greg Finak Cluster Merging for Flow Cytometry Data
flowPeaks Yongchao Ge An R package for flow data clustering
flowPloidy Tyler Smith Analyze flow cytometer data to determine sample ploidy
flowPlots N. Hawkins flowPlots: analysis plots and data class for gated flow cytometry data
FlowSOM Sofie Van Gassen Using self-organizing maps for visualization and interpretation of cytometry data
flowSpecs Jakob Theorell Tools for processing of high-dimensional cytometry data
flowStats Greg Finak, Mike Jiang 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
flowViz Mike Jiang Visualization for flow cytometry
flowVS Ariful Azad Variance stabilization in flow cytometry (and microarrays)
flowWorkspace Greg Finak, Mike Jiang Infrastructure for representing and interacting with 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 Models
fobitools Pol Castellano-Escuder Tools for Manipulating the 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
FuseSOM Elijah Willie A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets
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
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
gatom Alexey Sergushichev Finding an Active Metabolic Module in Atom Transition Network
GBScleanR Tomoyuki Furuta Error correction tool for noisy genotyping by sequencing (GBS) data
gcapc Mingxiang Teng GC Aware Peak Caller
gcatest Alejandro Ochoa 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
GDCRNATools Ruidong Li, Han Qu GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
gDNAx Robert Castelo Diagnostics for assessing genomic DNA contamination in RNA-seq data
gDR Arkadiusz Gladki Umbrella package for R packages in the gDR suite
gDRcore Arkadiusz Gladki Processing functions and interface to process and analyze drug dose-response data
gDRimport Arkadiusz Gladki Package for handling the import of dose-response data
gDRstyle Arkadiusz Gladki A package with style requirements for the gDR suite
gDRutils Arkadiusz Gladki A package with helper functions for processing drug response data
GDSArray Qian Liu Representing GDS files as array-like objects
gdsfmt Xiuwen Zheng R Interface to CoreArray Genomic Data Structure (GDS) Files
GeDi Annekathrin Nedwed Defining and visualizing the distances between different genesets
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
gemma.R Ogan Mancarci A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses
genArise IFC Development Team Microarray Analysis tool
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
genomation Altuna Akalin, Vedran Franke, Katarzyna Wreczycka Summary, annotation and visualization of genomic data
GenomAutomorphism Robersy Sanchez Compute the automorphisms between DNA's Abelian group representations
GenomeInfoDb Hervé Pagès 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 Hervé Pagès Representation and manipulation of short genomic alignments
GenomicDataCommons Sean Davis NIH / NCI Genomic Data Commons Access
GenomicDistributions Kristyna Kupkova GenomicDistributions: fast analysis of genomic intervals with Bioconductor
GenomicFeatures H. Pagès Conveniently import and query gene models
GenomicFiles Bioconductor Package Maintainer Distributed computing by file or by range
genomicInstability Mariano Alvarez Genomic Instability estimation for scRNA-Seq
GenomicInteractionNodes Jianhong Ou A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data
GenomicInteractions Liz Ing-Simmons Utilities for handling genomic interaction data
GenomicOZone Hua Zhong, Mingzhou Song Delineate outstanding genomic zones of differential gene activity
GenomicPlot Shuye Pu Plot profiles of next generation sequencing data in genomic features
GenomicRanges Hervé Pagès 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
GenProSeq Dongmin Jung Generating Protein Sequences with Deep Generative Models
GenVisR Zachary Skidmore Genomic Visualizations in R
GeoDiff Nicole Ortogero Count model based differential expression and normalization on GeoMx RNA data
GEOexplorer Guy Hunt GEOexplorer: a webserver for gene expression analysis and visualisation
GEOfastq Alex Pickering Downloads ENA Fastqs With GEO Accessions
GEOmetadb Jack Zhu A compilation of metadata from NCBI GEO
GeomxTools Maddy Griswold NanoString GeoMx Tools
GEOquery Sean Davis Get data from NCBI Gene Expression Omnibus (GEO)
GEOsubmission Alexandre Kuhn Prepares microarray data for submission to GEO
GeoTcgaData Erqiang Hu Processing Various Types of Data on GEO and TCGA
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
gg4way Benjamin I Laufer 4way Plots of Differential Expression
ggbio Michael Lawrence Visualization tools for genomic data
ggcyto Mike Jiang Visualize Cytometry data with ggplot
ggkegg Noriaki Sato KEGG pathway visualization by ggplot2
ggmanh John Lee Visualization Tool for GWAS Result
ggmsa Lang Zhou Plot Multiple Sequence Alignment using 'ggplot2'
GGPA Dongjun Chung graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
ggsc Guangchuang Yu Visualizing Single Cell and Spatial Transcriptomics
ggspavis Lukas M. Weber Visualization functions for spatial transcriptomics data
ggtree Guangchuang Yu an R package for visualization of tree and annotation data
ggtreeDendro Guangchuang Yu Drawing 'dendrogram' using 'ggtree'
ggtreeExtra Shuangbin Xu An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"
ggtreeSpace Guangchuang Yu Visualizing Phylomorphospaces using 'ggtree'
GIGSEA Shijia Zhu Genotype Imputed Gene Set Enrichment Analysis
ginmappeR Fernando Sola Gene Identifier Mapper
gINTomics Angelo Velle Multi-Omics data integration
girafe J. Toedling Genome Intervals and Read Alignments for Functional Exploration
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 visualizations for gene expression analysis
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
GloScope William Torous Population-level Representation on scRNA-Seq data
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
GNOSIS Lydia King Genomics explorer using statistical and survival analysis in R
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
goSorensen Pablo Flores Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)
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
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)
gpls Bioconductor Package Maintainer Classification using generalized partial least squares
gpuMagic Jiefei Wang An openCL compiler with the capacity to compile R functions and run the code on GPU
GrafGen William Wheeler Classification of Helicobacter Pylori Genomes
GRaNIE Christian Arnold GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data
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 Matt Eldridge Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
GRmetrics Nicholas Clark, Mario Medvedovic Calculate growth-rate inhibition (GR) metrics
groHMM Tulip Nandu, W. Lee Kraus GRO-seq Analysis Pipeline
GSALightning Billy Heung Wing Chang Fast Permutation-based Gene Set Analysis
GSAR Yasir Rahmatallah, Galina Glazko Gene Set Analysis in R
GSCA Zhicheng Ji GSCA: Gene Set Context Analysis
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 Robert Castelo Gene Set Variation Analysis for Microarray and RNA-Seq Data
gtrellis Zuguang Gu Genome Level Trellis Layout
GUIDEseq Lihua Julie Zhu GUIDE-seq and PEtag-seq analysis pipeline
Guitar Jia Meng Guitar
Gviz Robert Ivanek Plotting data and annotation information along genomic coordinates
GWAS.BAYES Jacob Williams Bayesian analysis of Gaussian GWAS data
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
gypsum Aaron Lun Interface to the gypsum REST API
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
HarmonizR Simon Schlumbohm Handles missing values and makes more data available
Harshlight Maurizio Pellegrino A "corrective make-up" program for microarray chips
hca Martin Morgan Exploring the Human Cell Atlas Data Coordinating Platform
HDF5Array Hervé Pagès HDF5 backend for DelayedArray objects
HDTD Anestis Touloumis Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
hdxmsqc Oliver M. Crook An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments
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
hermes Daniel Sabanés Bové Preprocessing, analyzing, and reporting of RNA-seq data
HERON Sean McIlwain Hierarchical Epitope pROtein biNding
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
HicAggR Olivier Cuvier Set of 3D genomic interaction analysis tools
HiCBricks Koustav Pal Framework for Storing and Accessing Hi-C Data Through HDF Files
HiCcompare Mikhail Dozmorov HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
HiCDCPlus Merve Sahin Hi-C Direct Caller Plus
HiCDOC Maigné Élise A/B compartment detection and differential analysis
HiCExperiment Jacques Serizay Bioconductor class for interacting with Hi-C files in R
HiContacts Jacques Serizay Analysing cool files in R with HiContacts
HiCool Jacques Serizay HiCool
hicVennDiagram Jianhong Ou Venn Diagram for genomic interaction data
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 Copy number prediction with correction for GC and mappability bias for HTS data
hoodscanR Ning Liu Spatial cellular neighbourhood scanning in R
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
HPiP Matineh Rahmatbakhsh Host-Pathogen Interaction Prediction
HTqPCR Heidi Dvinge Automated analysis of high-throughput qPCR data
HTSeqGenie Jens Reeder A NGS analysis pipeline.
HTSFilter Andrea Rau Filter replicated high-throughput transcriptome sequencing data
HubPub Kayla Interdonato Utilities to create and use Bioconductor Hubs
HumanTranscriptomeCompendium VJ Carey Tools to work with a Compendium of 181000 human transcriptome sequencing studies
hummingbird Eleni Adam Bayesian Hidden Markov Model for the detection of differentially methylated regions
HybridExpress Fabricio Almeida-Silva Comparative analysis of RNA-seq data for hybrids and their progenitors
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
IFAA Zhigang Li Robust Inference for Absolute Abundance in Microbiome Analysis
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 Arkadiusz Gladki igvR: integrative genomics viewer
igvShiny Arkadiusz Gladki igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)
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
IMAS Seonggyun Han Integrative analysis of Multi-omics data for Alternative Splicing
imcRtools Daniel Schulz Methods for imaging mass cytometry data analysis
IMMAN Minoo Ashtiani Interlog protein network reconstruction by Mapping and Mining ANalysis
ImmuneSpaceR ImmuneSpace Package Maintainer A Thin Wrapper around the ImmuneSpace Data and Tools Portal
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
iNETgrate Habil Zare Integrates DNA methylation data with gene expression in a single gene network
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 Identify 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
INTACT Jeffrey Okamoto Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis
InTAD Konstantin Okonechnikov Search for correlation between epigenetic signals and gene expression in TADs
intansv Wen Yao Integrative analysis of structural variations
interacCircos Zhe Cui The Generation of Interactive Circos Plot
InteractionSet Aaron Lun Base Classes for Storing Genomic Interaction Data
InteractiveComplexHeatmap Zuguang Gu Make Interactive Complex Heatmaps
interactiveDisplay Bioconductor Package Maintainer Package for enabling powerful shiny web displays of Bioconductor objects
interactiveDisplayBase Bioconductor Package Maintainer Base package for enabling powerful shiny web displays of Bioconductor objects
InterCellar Marta Interlandi InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics
IntEREst Ali Oghabian, Mikko Frilander Intron-Exon Retention Estimator
InterMineR InterMine Team R Interface with InterMine-Powered Databases
IntOMICS Pacinkova Anna Integrative analysis of multi-omics data to infer regulatory networks
IntramiRExploreR Surajit Bhattacharya Predicting Targets for Drosophila Intragenic miRNAs
IONiseR Mike Smith Quality Assessment Tools for Oxford Nanopore MinION data
iPAC Gregory Ryslik Identification of Protein Amino acid Clustering
iPath Kenong Su iPath pipeline for detecting perturbed pathways at individual level
ipdDb Steffen Klasberg IPD IMGT/HLA and IPD KIR database for Homo sapiens
IPO Thomas Lieb Automated Optimization of XCMS Data Processing parameters
IRanges Hervé Pagès Foundation of integer range manipulation in Bioconductor
IRISFGM Yuzhou Chang Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq
ISAnalytics Giulia Pais 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
iSEEde Kevin Rue-Albrecht iSEE extension for panels related to differential expression analysis
iSEEfier Najla Abassi Streamlining the creation of initial states for starting an iSEE instance
iSEEhex Kevin Rue-Albrecht iSEE extension for summarising data points in hexagonal bins
iSEEhub Kevin Rue-Albrecht iSEE for the Bioconductor ExperimentHub
iSEEindex Kevin Rue-Albrecht iSEE extension for a landing page to a custom collection of data sets
iSEEpathways Kevin Rue-Albrecht iSEE extension for panels related to pathway analysis
iSEEu Kevin Rue-Albrecht iSEE Universe
iSeq Qianxing Mo Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
ISLET Hao Feng Individual-Specific ceLl typE referencing Tool
isobar Florian P Breitwieser Analysis and quantitation of isobarically tagged MSMS proteomics data
IsoBayes Simone Tiberi IsoBayes: Single Isoform protein inference Method via Bayesian Analyses
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 Isoform Switches with Functional Consequences from both short- and long-read RNA-seq 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
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
katdetectr Daan Hazelaar Detection, Characterization and Visualization of Kataegis in Sequencing 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
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
knowYourCG Goldberg David Functional analysis of DNA methylome datasets
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
lemur Constantin Ahlmann-Eltze Latent Embedding Multivariate Regression
les Julian Gehring Identifying Differential Effects in Tiling Microarray Data
levi Jose Luiz Rybarczyk Filho Landscape Expression Visualization Interface
lfa Alejandro Ochoa 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
limpca Manon Martin An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family of methods
lineagespot Nikolaos Pechlivanis Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing
LinkHD "Laura M Zingaretti" LinkHD: a versatile framework to explore and integrate heterogeneous data
Linnorm Shun Hang Yip Linear model and normality based normalization and transformation method (Linnorm)
LinTInd Luyue Wang Lineage tracing by indels
lionessR Ping-Han Hsieh Modeling networks for individual samples using LIONESS
lipidr Ahmed Mohamed Data Mining and Analysis of Lipidomics Datasets
LiquidAssociation Yen-Yi Ho LiquidAssociation
lisaClust Ellis Patrick lisaClust: Clustering of Local Indicators of Spatial Association
lmdme Cristobal Fresno Linear Model decomposition for Designed Multivariate Experiments
LOBSTAHS Henry Holm, Daniel Lowenstein, James Collins Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
loci2path Tianlei Xu Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
logicFS Holger Schwender Identification of SNP Interactions
LOLA Nathan Sheffield Locus overlap analysis for enrichment of genomic ranges
LoomExperiment Bioconductor Package Maintainer LoomExperiment container
LPE Nitin Jain Methods for analyzing microarray data using Local Pooled Error (LPE) method
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
lute Sean K Maden Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments
LymphoSeq David Coffey Analyze high-throughput sequencing of T and B cell receptors
M3C Christopher John Monte Carlo Reference-based Consensus Clustering
M3Drop Tallulah Andrews Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
m6Aboost You Zhou m6Aboost
Maaslin2 Lauren McIver "Multivariable Association Discovery in Population-scale Meta-omics Studies"
Macarron Sagun Maharjan Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets
maCorrPlot Alexander Ploner Visualize artificial correlation in microarray 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
magpie Daoyu Duan MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation
magrene Fabrício Almeida-Silva Motif Analysis In Gene Regulatory Networks
MAI Jonathan Dekermanjian Mechanism-Aware Imputation
maigesPack Gustavo H. Esteves Functions to handle cDNA microarray data, including several methods of data analysis
MAIT Pol Sola-Santos Statistical Analysis of Metabolomic Data
makecdfenv James W. MacDonald CDF Environment Maker
MANOR Pierre Neuvial CGH Micro-Array NORmalization
MantelCorr Brian Steinmeyer Compute Mantel Cluster Correlations
MAPFX Hsiao-Chi Liao MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments
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
mariner Eric Davis Mariner: Explore the Hi-Cs
marr Tusharkanti Ghosh Maximum rank reproducibility
marray Yee Hwa (Jean) Yang Exploratory analysis for two-color spotted microarray data
martini Hector Climente-Gonzalez GWAS Incorporating Networks
maser Diogo F.T. Veiga Mapping Alternative Splicing Events to pRoteins
maSigPro Maria Jose Nueda Significant Gene Expression Profile Differences in Time Course Gene Expression Data
maskBAD Michael Dannemann Masking probes with binding affinity differences
MassArray Reid F. Thompson Analytical Tools for MassArray Data
massiR Sam Buckberry massiR: MicroArray Sample Sex Identifier
MassSpecWavelet Sergio Oller Moreno Peak Detection for Mass Spectrometry data using wavelet-based algorithms
MAST Andrew McDavid Model-based Analysis of Single Cell Transcriptomics
mastR Jinjin Chen Markers Automated Screening Tool in R
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 Scientific computing for out-of-memory signals and images
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 Bo Yao MBCB (Model-based Background Correction for Beadarray)
MBECS Michael Olbrich Evaluation and correction of batch effects in microbiome data-sets
mbkmeans Davide Risso Mini-batch K-means Clustering for Single-Cell RNA-seq
mBPCR P.M.V. Rancoita Bayesian Piecewise Constant Regression for DNA copy number estimation
MBQN Eva Brombacher Mean/Median-balanced quantile normalization
mbQTL Mercedeh Movassagh mbQTL: A package for SNP-Taxa mGWAS analysis
MBttest Yuan-De Tan Multiple Beta t-Tests
MCbiclust Robert Bentham Massive correlating biclusters for gene expression data and associated methods
mCSEA Jordi Martorell-Marugán Methylated CpGs Set Enrichment Analysis
mdp Helder Nakaya Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
mdqc Gabriela Cohen-Freue Mahalanobis Distance Quality Control for microarrays
MDTS Jack M.. Fu Detection of de novo deletion in targeted sequencing trios
MEAL Xavier Escribà Montagut Perform methylation analysis
MeasurementError.cor Beiying Ding Measurement Error model estimate for correlation coefficient
MEAT Sarah Voisin Muscle Epigenetic Age Test
MEB Jiadi Zhu, Yan Zhou A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq and scRNA-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 MEIGOR - 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
metabCombiner Hani Habra Method for Combining LC-MS Metabolomics Feature Measurements
metabinR Anestis Gkanogiannis Abundance and Compositional Based Binning of Metagenomes
MetaboAnnotation Johannes Rainer Utilities for Annotation of Metabolomics Data
MetaboCoreUtils Johannes Rainer Core Utils for Metabolomics Data
metabolomicsWorkbenchR Gavin Rhys Lloyd Metabolomics Workbench in R
metabomxtr Michael Nodzenski A package to run mixture models for truncated metabolomics data with normal or lognormal distributions
MetaboSignal Andrea Rodriguez-Martinez, Rafael Ayala MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
metaCCA Anna Cichonska Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
MetaCyto Zicheng Hu MetaCyto: A package for meta-analysis of cytometry data
metagene Charles Joly Beauparlant A package to produce metagene plots
metagene2 Eric Fournier A package to produce metagene plots
metagenomeSeq Joseph N. Paulson Statistical analysis for sparse high-throughput sequencing
metahdep John R. Stevens Hierarchical Dependence in Meta-Analysis
metaMS Yann Guitton MS-based metabolomics annotation pipeline
MetaNeighbor Stephan Fischer Single cell replicability analysis
MetaPhOR Emily Isenhart Metabolic Pathway Analysis of RNA
metapod Aaron Lun Meta-Analyses on P-Values of Differential Analyses
metapone Tianwei Yu Conducts pathway test of metabolomics data using a weighted permutation test
metaSeq Koki Tsuyuzaki Meta-analysis of RNA-Seq count data in multiple studies
metaseqR2 Panagiotis Moulos An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
MetaVolcanoR Cesar Prada Gene Expression Meta-analysis Visualization Tool
MetCirc Thomas Naake Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data
methimpute Aaron Taudt Imputation-guided re-construction of complete methylomes from WGBS data
methInheritSim Pascal Belleau Simulating Whole-Genome Inherited Bisulphite Sequencing Data
methodical Richard Heery Discovering genomic regions where methylation is strongly associated with transcriptional activity
MethPed Helena Carén A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
MethReg Tiago Silva Assessing the regulatory potential of DNA methylation regions or sites on gene transcription
methrix Anand Mayakonda Fast and efficient summarization of generic bedGraph files from Bisufite sequencing
MethTargetedNGS Muhammad Ahmer Jamil Perform Methylation Analysis on Next Generation Sequencing Data
MethylAid L.J.Sinke Visual and interactive quality control of large Illumina DNA Methylation array data sets
methylCC Stephanie C. Hicks Estimate the cell composition of whole blood in DNA methylation samples
methylclock Dolors Pelegri-Siso Methylclock - DNA methylation-based clocks
methylGSA Xu Ren Gene Set Analysis Using the Outcome of Differential Methylation
methyLImp2 Anna Plaksienko Missing value estimation of DNA methylation data
methylInheritance Astrid Deschênes Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
methylKit Altuna Akalin, Alexander Blume 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 Mattia Furlan Base resolution DNA methylation data analysis
methylscaper Rhonda Bacher 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
MGnifyR Tuomas Borman R interface to EBI MGnify metagenomics resource
mgsa Sebastian Bauer Model-based gene set analysis
mia Tuomas Borman Microbiome analysis
miaSim Yagmur Simsek Microbiome Data Simulation
miaViz Tuomas Borman Microbiome Analysis Plotting and Visualization
MiChip Jonathon Blake MiChip Parsing and Summarizing Functions
microbiome Leo Lahti Microbiome Analytics
microbiomeDASim Justin Williams Microbiome Differential Abundance Simulation
microbiomeExplorer Janina Reeder Microbiome Exploration App
microbiomeMarker Yang Cao microbiome biomarker analysis toolkit
MicrobiomeProfiler Meijun Chen An R/shiny package for microbiome functional enrichment analysis
MicrobiotaProcess Shuangbin Xu A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
microRNA "James F. Reid" Data and functions for dealing with microRNAs
microSTASIS Pedro Sánchez-Sánchez Microbiota STability ASsessment via Iterative cluStering
MICSQTL Qian Li MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)
midasHLA Maciej Migdał R package for immunogenomics data handling and association analysis
miloR Mike Morgan Differential neighbourhood abundance testing on a graph
mimager Aaron Wolen mimager: The Microarray Imager
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
MIRit Jacopo Ronchi Integrate microRNA and gene expression to decipher pathway complexity
miRLAB Thuc Duy Le Dry lab for exploring miRNA-mRNA relationships
miRmine Dusan Randjelovic Data package with miRNA-seq datasets from miRmine database as RangedSummarizedExperiment
miRNAmeConverter Stefan J. Haunsberger Convert miRNA Names to Different miRBase Versions
miRNApath James M. Ward miRNApath: Pathway Enrichment for miRNA Expression Data
miRNAtap 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 regulation
mirTarRnaSeq Mercedeh Movassagh mirTarRnaSeq
missMethyl Belinda Phipson, Jovana Maksimovic, Andrew Lonsdale Analysing Illumina HumanMethylation BeadChip Data
missRows Gonzalez Ignacio Handling Missing Individuals in Multi-Omics Data Integration
mistyR Jovan Tanevski Multiview Intercellular SpaTial modeling framework
mitch Mark Ziemann Multi-Contrast Gene Set Enrichment Analysis
mitoClone2 Benjamin Story Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations
mixOmics Max Bladen Omics Data Integration Project
MLInterfaces Vincent 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
mobileRNA Katie Jeynes-Cupper mobileRNA: Investigate the RNA mobilome & population-scale changes
MobilityTransformR Liesa Salzer Effective mobility scale transformation of CE-MS(/MS) data
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 Ricard Argelaguet 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
MoleculeExperiment Shila Ghazanfar Prioritising a molecule-level storage of Spatial Transcriptomics Data
MOMA Sunny Jones Multi Omic Master Regulator Analysis
monaLisa Michael Stadler Binned Motif Enrichment Analysis and Visualization
monocle Cole Trapnell Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Moonlight2R Matteo Tiberti Identify oncogenes and tumor suppressor genes from omics data
MoonlightR Matteo Tiberti Identify oncogenes and tumor suppressor genes from omics data
mosaics Dongjun Chung MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
mosbi Tim Daniel Rose Molecular Signature identification using Biclustering
mosdef Federico Marini MOSt frequently used and useful Differential Expression Functions
MOSim Sonia Tarazona Multi-Omics Simulation (MOSim)
Motif2Site Peyman Zarrineh Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions
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
motifTestR Stevie Pederson Perform key tests for binding motifs in sequence data
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
MSA2dist Kristian K Ullrich MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
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
MsBackendMsp Johannes Rainer Mass Spectrometry Data Backend for NIST msp Files
MsBackendRawFileReader Christian Panse Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
MsBackendSql Johannes Rainer SQL-based Mass Spectrometry Data Backend
MsCoreUtils RforMassSpectrometry Package Maintainer Core Utils for Mass Spectrometry Data
MsDataHub Laurent Gatto Mass Spectrometry Data on ExperimentHub
MsExperiment Laurent Gatto Infrastructure for Mass Spectrometry Experiments
MsFeatures Johannes Rainer Functionality for Mass Spectrometry Features
msgbsR Benjamin Mayne msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions
msImpute Soroor Hediyeh-zadeh Imputation of label-free mass spectrometry peptides
mslp Chunxuan Shao Predict synthetic lethal partners of tumour mutations
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
MsQuality Thomas Naake MsQuality - Quality metric calculation from Spectra and MsExperiment objects
MSstats Meena Choi Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
MSstatsBig Mateusz Staniak MSstats Preprocessing for Larger than Memory Data
MSstatsConvert Mateusz Staniak Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format
MSstatsLiP Devon Kohler LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
MSstatsLOBD Devon Kohler Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)
MSstatsPTM Devon Kohler Statistical Characterization of Post-translational Modifications
MSstatsQC Eralp Dogu Longitudinal system suitability monitoring and quality control for proteomic experiments
MSstatsQCgui Eralp Dogu A graphical user interface for MSstatsQC package
MSstatsShiny Devon Kohler MSstats GUI for Statistical Anaylsis of Proteomics Experiments
MSstatsTMT Devon Kohler Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
MuData Danila Bredikhin Serialization for MultiAssayExperiment Objects
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 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
MultimodalExperiment Lucas Schiffer Integrative Bulk and Single-Cell Experiment Container
multiOmicsViz Jing Wang Plot the effect of one omics data on other omics data along the chromosome
MultiRNAflow Rodolphe Loubaton An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions
multiscan Mizanur Khondoker R package for combining multiple scans
multistateQTL Amelia Dunstone Toolkit for the analysis of multi-state QTL data
multiWGCNA Dario Tommasini multiWGCNA
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 Joshua D. Campbell Mutational Signature Comprehensive Analysis Toolkit
MutationalPatterns Mark van Roosmalen Comprehensive genome-wide analysis of mutational processes
MVCClass Elizabeth Whalen Model-View-Controller (MVC) Classes
MWASTools Andrea Rodriguez-Martinez, Rafael Ayala MWASTools: an integrated pipeline to perform metabolome-wide association studies
mygene Adam Mark, Cyrus Afrasiabi, Chunlei Wu Access MyGene.Info_ services
myvariant Adam Mark, Chunlei Wu Accesses variant query and annotation services
mzID Laurent Gatto An mzIdentML parser for R
mzR Steffen Neumann parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
NADfinder Jianhong Ou, Lihua Julie Zhu Call wide peaks for sequencing data
NanoMethViz Shian Su Visualise methylation data from Oxford Nanopore sequencing
NanoStringDiff tingting zhai,hong wang Differential Expression Analysis of NanoString nCounter Data
NanoStringNCTools Maddy Griswold NanoString nCounter Tools
nanotatoR Surajit Bhattacharya Next generation structural variant annotation and classification
NanoTube Caleb Class An Easy Pipeline for NanoString nCounter Data Analysis
NBAMSeq Xu Ren Negative Binomial Additive Model for RNA-Seq Data
ncdfFlow Mike Jiang 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
NetActivity Carlos Ruiz-Arenas Compute gene set scores from a deep learning framework
netboost Pascal Schlosser Network Analysis Supported by Boosting
netDx Shraddha Pai Network-based patient classifier
nethet Nicolas Staedler, Frank Dondelinger A bioconductor package for high-dimensional exploration of biological network heterogeneity
netOmics Antoine Bodein Multi-Omics (time-course) network-based integration and interpretation
NetPathMiner Ahmed Mohamed NetPathMiner for Biological Network Construction, Path Mining and Visualization
netprioR Fabian Schmich A model for network-based prioritisation of genes
netresponse Leo Lahti Functional Network Analysis
NetSAM Zhiao Shi Network Seriation And Modularization
netSmooth Jonathan Ronen Network smoothing for scRNAseq
netZooR Marouen Ben Guebila Unified methods for the inference and analysis of gene regulatory networks
NeuCA Hao Feng NEUral network-based single-Cell Annotation tool
NewWave Federico Agostinis Negative binomial model for scRNA-seq
ngsReports Stevie Pederson Load FastqQC reports and other NGS related files
nipalsMCIA Maximilian Mattessich Multiple Co-Inertia Analysis via the NIPALS Method
nnNorm Adi Laurentiu Tarca Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
nnSVG Lukas M. Weber Scalable identification of spatially variable genes in spatially-resolved transcriptomics data
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 Deschênes Generate synthetic nucleosome maps
nucleR Alba Sala Nucleosome positioning package for R
nuCpos Hiroaki Kato An R package for prediction of nucleosome positions
nullranges Michael Love Generation of null ranges via bootstrapping or covariate matching
NuPoP Ji-Ping Wang An R package for nucleosome positioning prediction
occugene Oliver Will Functions for Multinomial Occupancy Distribution
OCplus Alexander Ploner Operating characteristics plus sample size and local fdr for microarray experiments
octad E. Chekalin Open Cancer TherApeutic Discovery (OCTAD)
odseq José Jiménez Outlier detection in multiple sequence alignments
OGRE Sven Berres Calculate, visualize and analyse overlap between genomic regions
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
omada Sokratis Kariotis Machine learning tools for automated transcriptome clustering analysis
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
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
omicsViewer Chen Meng Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omicsViewer
Omixer Lucy Sinke Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies
OmnipathR Denes Turei OmniPath web service client and more
ompBAM Alex Chit Hei Wong C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files
oncomix Daniel Pique Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data
oncoscanR Yann Christinat Secondary analyses of CNV data (HRD and more)
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 rate control
ontoProc Vincent Carey processing of ontologies of anatomy, cell lines, and so on
openCyto Mike Jiang Hierarchical Gating Pipeline for flow cytometry data
openPrimeR Matthias Döring Multiplex PCR Primer Design and Analysis
openPrimeRui Matthias Döring Shiny Application for Multiplex PCR Primer Design and Analysis
OpenStats Marina Kan A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association
oposSOM Henry Loeffler-Wirth Comprehensive analysis of transcriptome data
oppar Soroor Hediyeh zadeh Outlier profile and pathway analysis in R
oppti Abdulkadir Elmas Outlier Protein and Phosphosite Target Identifier
optimalFlow Hristo Inouzhe optimalFlow
OPWeight Mohamad Hasan Optimal p-value weighting with independent information
OrderedList Claudio Lottaz Similarities of Ordered Gene Lists
ORFhunteR Vasily V. Grinev Predict open reading frames in nucleotide sequences
ORFik Haakon Tjeldnes Open Reading Frames in Genomics
Organism.dplyr Martin Morgan dplyr-based Access to Bioconductor Annotation Resources
OrganismDbi Bioconductor Package Maintainer Software to enable the smooth interfacing of different database packages
orthogene Brian Schilder Interspecies gene mapping
orthos Panagiotis Papasaikas `orthos` is an R package for variance decomposition using conditional variational auto-encoders
OSAT Li Yan OSAT: Optimal Sample Assignment Tool
Oscope Ning Leng Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
OTUbase Daniel Beck Provides structure and functions for the analysis of OTU data
OUTRIDER Christian Mertes OUTRIDER - OUTlier in RNA-Seq fInDER
OutSplice Theresa Guo Comparison of Splicing Events between Tumor and Normal Samples
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
pairedGSEA Søren Helweg Dam Paired DGE and DGS analysis for gene set enrichment analysis
pairkat Max McGrath PaIRKAT
pandaR Joseph N. Paulson, Dan Schlauch PANDA Algorithm
panelcn.mops Gundula Povysil CNV detection tool for targeted NGS panel data
PanomiR Pourya Naderi Detection of miRNAs that regulate interacting groups of pathways
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
PanViz Luca Anholt Integrating Multi-Omic Network Data With Summay-Level GWAS Data
pareg Kim Philipp Jablonski Pathway enrichment using a regularized regression approach
parglms VJ Carey support for parallelized estimation of GLMs/GEEs
parody Vince Carey Parametric And Resistant Outlier DYtection
partCNV Ziyi Li Infer locally aneuploid cells using single cell RNA-seq data
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
pathlinkR Travis Blimkie Analyze and interpret RNA-Seq results
PathNet Ludwig Geistlinger An R package for pathway analysis using topological information
PathoStat Solaiappan Manimaran, Yue Zhao PathoStat Statistical Microbiome Analysis Package
pathRender Vince Carey Render molecular pathways
pathVar Samuel Zimmerman Methods to Find Pathways with Significantly Different Variability
pathview Weijun Luo a tool set for pathway based data integration and visualization
pathwayPCA Gabriel Odom Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
paxtoolsr Augustin Luna Access Pathways from Multiple Databases Through BioPAX and Pathway Commons
pcaExplorer Federico Marini Interactive Visualization of RNA-seq Data Using a Principal Components Approach
pcaMethods Henning Redestig A collection of PCA methods
PCAN Matthew Page and Patrice Godard Phenotype Consensus ANalysis (PCAN)
PCAtools Kevin Blighe PCAtools: Everything Principal Components Analysis
pcxn Sokratis Kariotis Exploring, analyzing and visualizing functions utilizing the pcxnData package
PDATK Benjamin Haibe-Kains Pancreatic Ductal Adenocarcinoma Tool-Kit
pdInfoBuilder Benilton Carvalho Platform Design Information Package Builder
PeacoQC Annelies Emmaneel Peak-based selection of high quality cytometry data
peakPantheR Arnaud Wolfer Peak Picking and Annotation of High Resolution Experiments
PECA Tomi Suomi Probe-level Expression Change Averaging
peco Chiaowen Joyce Hsiao A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
Pedixplorer Louis Le Nézet Pedigree Functions
pengls Stijn Hawinkel Fit Penalised Generalised Least Squares models
PepsNMR Manon Martin Pre-process 1H-NMR FID signals
pepStat Gregory C Imholte Statistical analysis of peptide microarrays
pepXMLTab Xiaojing Wang Parsing pepXML files and filter based on peptide FDR.
PERFect Quy Cao Permutation filtration for microbiome data
periodicDNA Jacques Serizay Set of tools to identify periodic occurrences of k-mers in DNA sequences
pfamAnalyzeR Kristoffer Vitting-Seerup Identification of domain isotypes in pfam data
pgca Gabriela Cohen-Freue PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data
pgxRpi Hangjia Zhao R wrapper for Progenetix
phantasus Alexey Sergushichev Visual and interactive gene expression analysis
phantasusLite Alexey Sergushichev Loading and annotation RNA-seq counts matrices
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
phenomis Etienne A. Thevenot Postprocessing and univariate analysis of omics data
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
PIPETS Quinlan Furumo Poisson Identification of PEaks from Term-Seq data
PIUMA Mattia Chiesa Phenotypes Identification Using Mapper from topological data Analysis
planet Victor Yuan Placental DNA methylation analysis tools
planttfhunter Fabrício Almeida-Silva Identification and classification of plant transcription factors
plasmut Adith Arun Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic
plgem Norman Pavelka Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
plier Crispin Miller Implements the Affymetrix PLIER algorithm
PloGO2 Jemma Wu, Dana Pascovici Plot Gene Ontology and KEGG pathway Annotation and Abundance
plotgardener Nicole Kramer, Douglas Phanstiel Coordinate-Based Genomic Visualization Package for R
plotGrouper John D. Gagnon Shiny app GUI wrapper for ggplot with built-in statistical analysis
PLPE Soo-heang Eo Local Pooled Error Test for Differential Expression with Paired High-throughput Data
PLSDAbatch Yiwen (Eva) Wang PLSDA-batch
plyinteractions Jacques Serizay Extending tidy verbs to genomic interactions
plyranges Michael Love A fluent interface for manipulating GenomicRanges
pmm Anna Drewek Parallel Mixed Model
pmp Gavin Rhys Lloyd Peak Matrix Processing and signal batch correction for metabolomics datasets
PoDCall Hans Petter Brodal Positive Droplet Calling for DNA Methylation Droplet Digital PCR
podkat Ulrich Bodenhofer Position-Dependent Kernel Association Test
pogos VJ Carey PharmacOGenomics Ontology Support
polyester Jack Fu, Jeff Leek Simulate RNA-seq reads
POMA Pol Castellano-Escuder Tools for Omics Data 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
pqsfinder Jiri Hon Identification of potential quadruplex forming sequences
pram Peng Liu Pooling RNA-seq datasets for assembling transcript models
prebs Karolis Uziela Probe region expression estimation for RNA-seq data for improved microarray comparability
preciseTAD Mikhail Dozmorov preciseTAD: A machine learning framework for precise TAD boundary prediction
PREDA Francesco Ferrari Position Related Data Analysis
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
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
profileplyr Tom Carroll, Doug Barrows Visualization and annotation of read signal over genomic ranges with profileplyr
profileScoreDist Paal O. Westermark Profile score distributions
progeny Aurélien Dugourd Pathway RespOnsive GENes for activity inference from gene expression
projectR Genevieve Stein-O'Brien Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering
pRoloc Laurent Gatto A unifying bioinformatics framework for spatial proteomics
pRolocGUI Lisa Breckels Interactive visualisation of spatial proteomics data
PROMISE Stan Pounds, Xueyuan Cao PRojection Onto the Most Interesting Statistical Evidence
PROPER Hao Wu PROspective Power Evaluation for RNAseq
PROPS Lichy Han PRObabilistic Pathway Score (PROPS)
Prostar Samuel Wieczorek Provides a GUI for DAPAR
proteasy Martin Rydén Protease Mapping
proteinProfiles Julian Gehring Protein Profiling
ProteoDisco Job van Riet Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences
ProteoMM Yuliya V Karpievitch Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform
protGear Kennedy Mwai Protein Micro Array Data Management and Interactive Visualization
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
PSMatch Laurent Gatto Handling and Managing Peptide Spectrum Matches
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
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
pwalign Hervé Pagès Perform pairwise sequence alignments
PWMEnrich Diego Diez PWM enrichment analysis
pwOmics Torsten Schoeps Pathway-based data integration of omics data
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
qmtools Jaehyun Joo Quantitative Metabolomics Data Processing Tools
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 quantitative proteomics data analysis
qsea Matthias Lienhard IP-seq data analysis and vizualization
qsmooth Stephanie C. Hicks Smooth quantile normalization
QSutils Mercedes Guerrero-Murillo Quasispecies Diversity
qsvaR Hedia Tnani Generate Quality Surrogate Variable Analysis for Degradation Correction
QTLExperiment Amelia Dunstone S4 classes for QTL summary statistics and metadata
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
raer Kent Riemondy RNA editing tools in R
RaggedExperiment Marcel Ramos Representation of Sparse Experiments and Assays Across Samples
RAIDS Pascal Belleau Accurate Inference of Genetic Ancestry from Cancer Sequences
rain Paul F. Thaben Rhythmicity Analysis Incorporating Non-parametric Methods
ramr Oleksii Nikolaienko Detection of Rare Aberrantly Methylated Regions in Array and NGS Data
ramwas Andrey A Shabalin Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
RandomWalkRestartMH Alberto Valdeolivas Random walk with restart on multiplex and heterogeneous Networks
randPack Robert Gentleman Randomization routines for Clinical Trials
randRotation Peter Hettegger Random Rotation Methods for High Dimensional Data with Batch Structure
RankProd Francesco Del Carratore Rank Product method for identifying differentially expressed genes with application in meta-analysis
RAREsim Ryan Barnard Simulation of Rare Variant Genetic Data
RareVariantVis Tomasz Stokowy A suite for analysis of rare genomic variants in whole genome sequencing data
Rarr Mike Smith Read Zarr Files in R
rawDiag Christian Panse Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful
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
RBioFormats Andrzej Oleś R interface to Bio-Formats
RBioinf Robert Gentleman RBioinf
rBiopaxParser Frank Kramer Parses BioPax files and represents them in R
rBLAST Michael Hahsler R Interface for the Basic Local Alignment Search Tool
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
Rbwa Jean-Philippe Fortin R wrapper for BWA-backtrack and BWA-MEM aligners
RCAS Bora Uyar RNA Centric Annotation System
RCASPAR Douaa Mugahid, Lars Kaderali A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
rcellminer Augustin Luna, Vinodh Rajapakse, Fathi Elloumi rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
rCGH Frederic Commo Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
RcisTarget Gert Hulselmans RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions
RCM Stijn Hawinkel Fit row-column association models with the negative binomial distribution for the microbiome
Rcollectl Vincent Carey Help use collectl with R in Linux, to measure resource consumption in R processes
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
RCX Florian Auer R package implementing the Cytoscape Exchange (CX) format
RCy3 Alex Pico Functions to Access and Control Cytoscape
RCyjs Paul Shannon Display and manipulate graphs in cytoscape.js
rDGIdb Lars Bosshard R Wrapper for DGIdb
Rdisop Steffen Neumann Decomposition of Isotopic Patterns
RDRToolbox Christoph Bartenhagen A package for nonlinear dimension reduction with Isomap and LLE.
ReactomeContentService4R Chi-Lam Poon Interface for the Reactome Content Service
ReactomeGraph4R Chi-Lam Poon Interface for the Reactome Graph Database
ReactomeGSA Johannes Griss Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
ReactomePA Guangchuang Yu Reactome Pathway Analysis
ReadqPCR James Perkins Read qPCR data
REBET Bill Wheeler The subREgion-based BurdEn Test (REBET)
rebook Aaron Lun Re-using Content in Bioconductor Books
receptLoss Daniel Pique Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors
reconsi Stijn Hawinkel 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 public DNA methylation array data 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
RedisParam Martin Morgan Provide a 'redis' back-end for BiocParallel
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
regionalpcs Tiffany Eulalio Summarizing Regional Methylation with Regional Principal Components Analysis
RegionalST Ziyi Li Investigating regions of interest and performing cross-regional analysis with spatial transcriptomics data
regioneR Bernat Gel Association analysis of genomic regions based on permutation tests
regioneReloaded Roberto Malinverni RegioneReloaded: Multiple Association for Genomic Region Sets
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
RESOLVE Luca De Sano RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes
restfulSE Shweta Gopaulakrishnan Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
retrofit Adam Park RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics
ReUseData Qian Liu Reusable and reproducible Data Management
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
rGenomeTracks Omar Elashkar Integerated visualization of epigenomic data
RGMQL Simone Pallotta GenoMetric Query Language for R/Bioconductor
RgnTX Yue Wang Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity
rgoslin Nils Hoffmann Lipid Shorthand Name Parsing and Normalization
RGraph2js Stephane Cano Convert a Graph into a D3js Script
Rgraphviz Kasper Daniel Hansen Provides plotting capabilities for R graph objects
rGREAT Zuguang Gu GREAT Analysis - Functional Enrichment on Genomic Regions
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 HDF Scalable Data Service
rhdf5filters Mike Smith HDF5 Compression Filters
Rhdf5lib Mike Smith hdf5 library as an R package
Rhisat2 Charlotte Soneson R Wrapper for HISAT2 Aligner
Rhtslib Hervé Pagès HTSlib high-throughput sequencing library as an R package
RiboCrypt Michal Swirski Interactive visualization in genomics
RiboDiPA Ji-Ping Wang Differential pattern analysis for Ribo-seq data
RiboProfiling A. Popa Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
ribor Michael Geng An R Interface for Ribo Files
riboSeqR Samuel Granjeaud Analysis of sequencing data from ribosome profiling experiments
ribosomeProfilingQC Jianhong Ou Ribosome Profiling Quality Control
rifi Jens Georg 'rifi' analyses data from rifampicin time series created by microarray or RNAseq
rifiComparative Loubna Youssar 'rifiComparative' compares the output of rifi from two different conditions.
RImmPort Zicheng Hu, Ravi Shankar RImmPort: Enabling Ready-for-analysis Immunology Research Data
RIPAT Min-Jeong Baek Retroviral Integration Pattern Analysis Tool (RIPAT)
Risa Alejandra Gonzalez-Beltran Converting experimental metadata from ISA-tab into Bioconductor data structures
RITAN Michael Zimmermann Rapid Integration of Term Annotation and Network resources
RIVER Yungil Kim R package for RIVER (RNA-Informed Variant Effect on Regulation)
RJMCMCNucleosomes Astrid Deschênes Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
RLassoCox Wei Liu A reweighted Lasso-Cox by integrating gene interaction information
RLMM Nusrat Rabbee A Genotype Calling Algorithm for Affymetrix SNP Arrays
RLSeq Henry Miller RLSeq: An analysis package for R-loop mapping data
Rmagpie Camille Maumet MicroArray Gene-expression-based Program In Error rate estimation
RMassBank RMassBank at Eawag Workflow to process tandem MS files and build MassBank records
rmelting J. Aravind R Interface to MELTING 5
Rmmquant Zytnicki Matthias RNA-Seq multi-mapping Reads Quantification Tool
rmspc Meriem Bahda Multiple Sample Peak Calling
RNAAgeCalc Xu Ren A multi-tissue transcriptional age calculator
RNAdecay Reed Sorenson Maximum Likelihood Decay Modeling of RNA Degradation Data
rnaEditr Lanyu Zhang Statistical analysis of RNA editing sites and hyper-editing regions
RNAinteract Mike Smith Estimate Pairwise Interactions from multidimensional features
RNAmodR Felix G.M. Ernst Detection of post-transcriptional modifications in high throughput sequencing data
RNAmodR.AlkAnilineSeq Felix G.M. Ernst Detection of m7G, m3C and D modification by AlkAnilineSeq
RNAmodR.ML Felix G.M. Ernst Detecting patterns of post-transcriptional modifications using machine learning
RNAmodR.RiboMethSeq Felix G.M. Ernst Detection of 2'-O methylations by RiboMethSeq
RNAsense Marcus Rosenblatt Analysis of Time-Resolved RNA-Seq Data
rnaseqcomp Mingxiang Teng Benchmarks for RNA-seq Quantification Pipelines
RNAseqCovarImpute Brennan Baker Impute Covariate Data in RNA Sequencing Studies
RNASeqPower Terry M Therneau Sample size for RNAseq studies
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
roastgsa Adria Caballe Rotation based gene set analysis
ROC Vince Carey utilities for ROC, with microarray focus
ROCpAI Juan-Pedro Garcia Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers
RolDE Medical Bioinformatics Centre RolDE: Robust longitudinal Differential Expression
rols Laurent Gatto An R interface to the Ontology Lookup Service
ROntoTools Sorin Draghici 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
rprimer Sofia Persson Design Degenerate Oligos from a Multiple DNA Sequence Alignment
RProtoBufLib Mike Jiang C++ headers and static libraries of Protocol buffers
rpx Laurent Gatto R Interface to the ProteomeXchange Repository
Rqc Welliton Souza Quality Control Tool for High-Throughput Sequencing Data
rqt Ilya Y. Zhbannikov rqt: utilities for gene-level meta-analysis
rqubic Jitao David Zhang Qualitative biclustering algorithm for expression data analysis in R
rRDP Michael Hahsler Interface to the RDP Classifier
RRHO Jonathan Rosenblatt Inference on agreement between ordered lists
rrvgo Sergi Sayols Reduce + Visualize GO
Rsamtools Bioconductor Package Maintainer Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
rsbml Michael Lawrence R support for SBML, using libsbml
rScudo Matteo Ciciani Signature-based Clustering for Diagnostic Purposes
rsemmed Leslie Myint An interface to the Semantic MEDLINE database
RSeqAn August Guang R SeqAn
Rsubread Wei Shi, Yang Liao and Gordon K Smyth Mapping, quantification and variant analysis of sequencing data
RSVSim Christoph Bartenhagen RSVSim: an R/Bioconductor package for the simulation of structural variations
rSWeeP Danrley R. Fernandes Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
RTCA Jitao David Zhang Open-source toolkit to analyse data from xCELLigence System (RTCA)
RTCGA Marcin Kosinski The Cancer Genome Atlas Data Integration
RTCGAToolbox Marcel Ramos A new tool for exporting TCGA Firehose data
RTN Mauro Castro RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
RTNduals Mauro Castro, Clarice Groeneveld Analysis of co-regulation and inference of 'dual regulons'
RTNsurvival Clarice Groeneveld, Mauro A. A. Castro Survival analysis using transcriptional networks inferred by the RTN package
RTopper Luigi Marchionni This package is designed to perform Gene Set Analysis across multiple genomic platforms
Rtpca Nils Kurzawa Thermal proximity co-aggregation with R
rtracklayer Michael Lawrence R interface to genome annotation files and the UCSC genome browser
Rtreemix Jasmina Bogojeska Rtreemix: Mutagenetic trees mixture models.
rTRM Diego Diez Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks
rTRMui Diego Diez A shiny user interface for rTRM
runibic Patryk Orzechowski runibic: row-based biclustering algorithm for analysis of gene expression data in R
RUVcorr Saskia Freytag Removal of unwanted variation for gene-gene correlations and related analysis
RUVnormalize Laurent Jacob RUV for normalization of expression array data
RUVSeq Davide Risso Remove Unwanted Variation from RNA-Seq Data
Rvisdiff David Barrios Interactive Graphs for Differential Expression
RVS Alexandre Bureau Computes estimates of the probability of related individuals sharing a rare variant
rWikiPathways Egon Willighagen rWikiPathways - R client library for the WikiPathways API
S4Arrays Hervé Pagès Foundation of array-like containers in Bioconductor
S4Vectors Hervé Pagès Foundation of vector-like and list-like containers in Bioconductor
safe Ludwig Geistlinger Significance Analysis of Function and Expression
sagenhaft Tim Beissbarth Collection of functions for reading and comparing SAGE libraries
SAIGEgds Xiuwen Zheng Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies
sampleClassifier Khadija El Amrani Sample Classifier
SamSPECTRAL Habil Identifies cell population in flow cytometry data
sangeranalyseR Kuan-Hao Chao sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
sangerseqR Jonathon Hill Tools for Sanger Sequencing Data in R
SANTA Alex Cornish Spatial Analysis of Network Associations
SARC Krutik Patel Statistical Analysis of Regions with CNVs
sarks Dennis Wylie Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains
saseR Alexandre Segers Scalable Aberrant Splicing and Expression Retrieval
satuRn Jeroen Gilis Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
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
SCAN.UPC Stephen R. Piccolo Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
scanMiR Pierre-Luc Germain scanMiR
scanMiRApp Pierre-Luc Germain scanMiR shiny application
scAnnotatR Johannes Griss Pretrained learning models for cell type prediction on single cell RNA-sequencing data
SCANVIS Phaedra Agius SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
SCArray Xiuwen Zheng Large-scale single-cell omics data manipulation with GDS files
SCArray.sat Xiuwen Zheng Large-scale single-cell RNA-seq data analysis using GDS files and Seurat
scater Alan O'Callaghan Single-Cell Analysis Toolkit for Gene Expression Data in R
scatterHatch Atul Deshpande Creates hatched patterns for scatterplots
scBFA Ruoxin Li A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
SCBN Yan Zhou A statistical normalization method and differential expression analysis for RNA-seq data between different species
scBubbletree Simo Kitanovski Quantitative visual exploration of scRNA-seq data
scCB2 Zijian Ni CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
scClassify Yingxin Lin scClassify: single-cell Hierarchical Classification
sccomp Stefano Mangiola Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data
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
scDDboost Xiuyu Ma A compositional model to assess expression changes from single-cell rna-seq data
scde Evan Biederstedt Single Cell Differential Expression
scDesign3 Dongyuan Song A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics
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
scFeatures Yue Cao scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction
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
scider Yunshun Chen Spatial cell-type inter-correlation by density in R
scifer Rodrigo Arcoverde Cerveira Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences
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
scMET Andreas C. Kapourani Bayesian modelling of cell-to-cell DNA methylation heterogeneity
scmeth Divy Kangeyan Functions to conduct quality control analysis in methylation data
scMitoMut Wenjie Sun Single-cell Mitochondrial Mutation Analysis Tool
scMultiSim Hechen i Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell Interactions
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 Shian Su Pipeline for single cell multi-omic data pre-processing
scran Aaron Lun Methods for Single-Cell RNA-Seq Data Analysis
scReClassify Taiyun Kim scReClassify: post hoc cell type classification of single-cell RNA-seq data
scRecover Zhun Miao scRecover for imputation of single-cell RNA-seq data
screenCounter Aaron Lun Counting Reads in High-Throughput Sequencing Screens
ScreenR Emanuel Michele Soda Package to Perform High Throughput Biological Screening
scRepertoire Nick Borcherding A toolkit for single-cell immune receptor profiling
scRNAseqApp Jianhong Ou A single-cell RNAseq Shiny app-package
scruff Zhe Wang Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
scry Kelly Street Small-Count Analysis Methods for High-Dimensional Data
scShapes Malindrie Dharmaratne A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data
scTensor Koki Tsuyuzaki Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition
scTGIF Koki Tsuyuzaki Cell type annotation for unannotated single-cell RNA-Seq data
scTHI Michele Ceccarelli Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data
scTreeViz Jayaram Kancherla R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations
scuttle Aaron Lun Single-Cell RNA-Seq Analysis Utilities
scviR Vincent Carey experimental inferface from R to scvi-tools
SDAMS Yuntong Li Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data
sechm Pierre-Luc Germain sechm: Complex Heatmaps from a SummarizedExperiment
segmenter Mahmoud Ahmed Perform Chromatin Segmentation Analysis in R by Calling ChromHMM
segmentSeq Samuel Granjeaud 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
seq.hotSPOT Sydney Grant Targeted sequencing panel design based on mutation hotspots
seq2pathway Arjun Kinstlick a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data
seqArchR Sarvesh Nikumbh Identify Different Architectures of Sequence Elements
seqArchRplus Sarvesh Nikumbh Downstream analyses of promoter sequence architectures and HTML report generation
SeqArray Xiuwen Zheng Data Management of Large-Scale Whole-Genome Sequence Variant Calls
seqCAT Erik Fasterius High Throughput Sequencing Cell Authentication Toolkit
seqcombo Guangchuang Yu Visualization Tool for Genetic Reassortment
SeqGate Stéphanie Rialle Filtering of Lowly Expressed Features
SeqGSEA Xi Wang Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
seqLogo Robert Ivanek Sequence logos for DNA sequence alignments
seqPattern Vanja Haberle Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences
seqsetvis Joseph R Boyd Set Based Visualizations for Next-Gen Sequencing Data
SeqSQC Qian Liu A bioconductor package for sample quality check with next generation sequencing data
seqTools Wolfgang Kaisers Analysis of nucleotide, sequence and quality content on fastq files
SeqVarTools Stephanie M. Gogarten Tools for variant data
sesame Wanding Zhou SEnsible Step-wise Analysis of DNA MEthylation BeadChips
SEtools Pierre-Luc Germain SEtools: tools for working with SummarizedExperiment
sevenbridges Phil Webster 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
SGCP Niloofar AghaieAbiane SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expression networks
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
shiny.gosling Appsilon A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization for R and Shiny
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 Brendan Gongol Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
signeR Renan Valieris Empirical Bayesian approach to mutational signature discovery
signifinder Stefania Pirrotta Collection and implementation of public transcriptional cancer signatures
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
SimBu Alexander Dietrich Simulate Bulk RNA-seq Datasets from Single-Cell Datasets
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 Deschênes Metrics to estimate a level of similarity between two ChIP-Seq profiles
SIMLR Luca De Sano Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)
simona Zuguang Gu Semantic Similarity in Bio-Ontologies
simPIC Sagrika Chugh simPIC: flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data
simpleSeg Ellis Patrick A package to perform simple cell segmentation
simplifyEnrichment Zuguang Gu Simplify Functional Enrichment Results
sincell Miguel Julia, Antonio Rausell R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
single Rocio Espada Accurate consensus sequence from nanopore reads of a gene library
SingleCellAlleleExperiment Jonas Schuck S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes
SingleCellExperiment Davide Risso S4 Classes for Single Cell Data
SingleCellSignalR Jacques Colinge Developer Cell Signalling Using Single Cell RNAseq Data Analysis
singleCellTK Joshua David Campbell 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 Malvika Kharbanda Rank-based single-sample gene set scoring method
SiPSiC Daniel Davis Calculate Pathway Scores for Each Cell in scRNA-Seq Data
sitadela Panagiotis Moulos An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms
sitePath Chengyang Ji Phylogeny-based sequence clustering with site polymorphism
sizepower Weiliang Qiu Sample Size and Power Calculation in Micorarray Studies
sketchR Charlotte Soneson An R interface for python subsampling/sketching algorithms
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
slingshot Kelly Street Tools for ordering single-cell sequencing
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
smartid Jinjin Chen Scoring and Marker Selection Method Based on Modified TF-IDF
SMITE Neil Ari Wijetunga, Andrew Damon Johnston Significance-based Modules Integrating the Transcriptome and Epigenome
smoothclust Lukas M. Weber smoothclust
SNAGEE David Venet Signal-to-Noise applied to Gene Expression Experiments
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
SomaticSignatures Julian Gehring Somatic Signatures
SOMNiBUS Kathleen Klein Smooth modeling of bisulfite sequencing
SpaceMarkers Atul Deshpande Spatial Interaction Markers
SpacePAC Gregory Ryslik Identification of Mutational Clusters in 3D Protein Space via Simulation.
Spaniel Rachel Queen Spatial Transcriptomics Analysis
sparrow Steve Lianoglou Take command of set enrichment analyses through a unified interface
SparseArray Hervé Pagès High-performance sparse data representation and manipulation in R
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
spaSim Yuzhou Feng Spatial point data simulator for tissue images
SpatialCPie Joseph Bergenstraahle Cluster analysis of Spatial Transcriptomics data
spatialDE Gabriele Sales R wrapper for SpatialDE
SpatialDecon Maddy Griswold Deconvolution of mixed cells from spatial and/or bulk gene expression data
SpatialExperiment Dario Righelli S4 Class for Spatially Resolved -omics Data
SpatialFeatureExperiment Lambda Moses Integrating SpatialExperiment with Simple Features in sf
spatialHeatmap Jianhai Zhang spatialHeatmap
SpatialOmicsOverlay Maddy Griswold Spatial Overlay for Omic Data from Nanostring GeoMx Data
spatzie Jennifer Hammelman Identification of enriched motif pairs from chromatin interaction data
speckle Belinda Phipson Statistical methods for analysing single cell RNA-seq data
specL Christian Panse specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
SpeCond Florence Cavalli Condition specific detection from expression data
Spectra RforMassSpectrometry Package Maintainer Spectra Infrastructure for Mass Spectrometry Data
SpectralTAD Mikhail Dozmorov 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
SPIAT Yuzhou Feng Spatial Image Analysis of Tissues
spicyR Ellis Patrick Spatial analysis of in situ cytometry data
SpidermiR Claudia Cava SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data
spikeLI Enrico Carlon Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
spiky Tim Triche Spike-in calibration for cell-free MeDIP
spillR Marco Guazzini Spillover Compensation in Mass Cytometry Data
spkTools Matthew N McCall Methods for Spike-in Arrays
splatter Luke Zappia Simple Simulation of Single-cell RNA Sequencing Data
SpliceWiz Alex Chit Hei Wong interactive analysis and visualization of alternative splicing in R
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
spoon Kinnary Shah Address the Mean-variance Relationship in Spatial Transcriptomics Data
SpotClean Zijian Ni SpotClean adjusts for spot swapping in spatial transcriptomics data
SPOTlight Marc Elosua-Bayes `SPOTlight`: Spatial Transcriptomics Deconvolution
SpotSweeper Michael Totty Spatially-aware quality control for spatial transcriptomics
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 tables 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
srnadiff Zytnicki Matthias Finding differentially expressed unannotated genomic regions from RNA-seq data
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
sSNAPPY Wenjun Liu Single Sample directioNAl Pathway Perturbation analYsis
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
standR Ning Liu Spatial transcriptome analyses of Nanostring's DSP data in R
staRank Juliane Siebourg Stability Ranking
StarBioTrek Claudia Cava StarBioTrek
STATegRa David Gomez-Cabrero, Núria Planell Classes and methods for multi-omics data integration
Statial Farhan Ameen A package to identify changes in cell state relative to spatial associations
statTarget Hemi Luan Statistical Analysis of Molecular Profiles
STdeconvolve Brendan Miller Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data
stepNorm Yuanyuan Xiao Stepwise normalization functions for cDNA microarrays
stJoincount Jiarong Song stJoincount - Join count statistic for quantifying spatial correlation between clusters
strandCheckR Thu-Hien To Calculate strandness information of a bam file
Streamer Martin Morgan Enabling stream processing of large files
STRINGdb Damian Szklarczyk STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis
STROMA4 Sadiq Saleh Assign Properties to TNBC Patients
struct Gavin Rhys Lloyd Statistics in R Using Class-based Templates
Structstrings Felix G.M. Ernst Implementation of the dot bracket annotations with Biostrings
structToolbox Gavin Rhys Lloyd Data processing & analysis tools for Metabolomics and other omics
StructuralVariantAnnotation Daniel Cameron Variant annotations for structural variants
SubCellBarCode Taner Arslan SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome
subSeq Andrew J. Bass, John D. Storey Subsampling of high-throughput sequencing count data
SUITOR Bill Wheeler Selecting the number of mutational signatures through cross-validation
SummarizedBenchmark Patrick Kimes Classes and methods for performing benchmark comparisons
SummarizedExperiment Hervé Pagès SummarizedExperiment container
Summix Audrey Hendricks Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data
supersigs Albert Kuo Supervised mutational signatures
supraHex Hai Fang supraHex: a supra-hexagonal map for analysing tabular omics data
surfaltr Pooja Gangras Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr
SurfR Aurora Maurizio Surface Protein Prediction and Identification
survcomp Benjamin Haibe-Kains Performance Assessment and Comparison for Survival Analysis
survtype Dongmin Jung Subtype Identification with Survival Data
sva Jeffrey T. Leek, John D. Storey, W. Evan Johnson Surrogate Variable Analysis
svaNUMT Ruining Dong NUMT detection from structural variant calls
svaRetro Ruining Dong Retrotransposed transcript detection from structural variants
SVMDO Mustafa Erhan Ozer Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology
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
switchBox Bahman Afsari, Luigi Marchionni, Wikum Dinalankara Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
switchde Kieran Campbell Switch-like differential expression across single-cell trajectories
synapsis Lucy McNeill An R package to automate the analysis of double-strand break repair during meiosis
synapter Laurent Gatto Sebastian Gibb Label-free data analysis pipeline for optimal identification and quantitation
synergyfinder Shuyu Zheng Calculate and Visualize Synergy Scores for Drug Combinations
SynExtend Nicholas Cooley Tools for Working With Synteny Objects
synlet Chunxuan Shao Hits Selection for Synthetic Lethal RNAi Screen Data
SynMut Haogao Gu SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures
syntenet Fabrício Almeida-Silva Inference And Analysis Of Synteny Networks
systemPipeR Thomas Girke systemPipeR: workflow management and report generation environment
systemPipeShiny Le Zhang systemPipeShiny: An Interactive Framework for Workflow Management and Visualization
systemPipeTools Daniela Cassol Tools for data visualization
tadar Lachlan Baer Transcriptome Analysis of Differential Allelic Representation
TADCompare Mikhail Dozmorov TADCompare: Identification and characterization of differential TADs
tanggle Klaus Schliep Visualization of Phylogenetic Networks
TAPseq Andreas R. Gschwind Targeted scRNA-seq primer design for TAP-seq
target Mahmoud Ahmed Predict Combined Function of Transcription Factors
TargetDecoy Elke Debrie Diagnostic Plots to Evaluate the Target Decoy Approach
TargetScore Yue Li TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information
TargetSearch Alvaro Cuadros-Inostroza A package for the analysis of GC-MS metabolite profiling data
TBSignatureProfiler Aubrey R. 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
TCGAutils Marcel Ramos TCGA utility functions for data management
TCseq Mengjun Wu Time course sequencing data analysis
TDbasedUFE Y-h. Taguchi Tensor Decomposition Based Unsupervised Feature Extraction
TDbasedUFEadv Y-h. Taguchi Advanced package of tensor decomposition based unsupervised feature extraction
TEKRABber Yao-Chung Chen An R package estimates the correlations of orthologs and transposable elements between two species
TENxIO Marcel Ramos Import methods for 10X Genomics files
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
terraTCGAdata Marcel Ramos OpenAccess TCGA Data on Terra as MultiAssayExperiment
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 Gaia Ceddia Transcription Factor High Accumulation Zones
TFutils Vincent Carey TFutils
tidybulk Stefano Mangiola Brings transcriptomics to the tidyverse
tidyCoverage Jacques Serizay Extract and aggregate genomic coverage over features of interest
tidyomics Stefano Mangiola Easily install and load the tidyomics ecosystem
tidySingleCellExperiment Stefano Mangiola Brings SingleCellExperiment to the Tidyverse
tidySpatialExperiment William Hutchison Brings SpatialExperiment 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
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
tomoda Wendao Liu Tomo-seq data analysis
tomoseqr Ryosuke Matsuzawa R Package for Analyzing Tomo-seq Data
TOP Harry Robertson TOP Constructs Transferable Model Across Gene Expression Platforms
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)
tpSVG Boyi Guo Thin plate models to detect spatially variable genes
tracktables Tom Carroll Build IGV tracks and HTML reports
trackViewer Jianhong Ou A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data
tradeSeq Hector Roux de Bezieux trajectory-based differential expression analysis for sequencing data
TrajectoryGeometry Michael Shapiro This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns
TrajectoryUtils Aaron Lun Single-Cell Trajectory Analysis Utilities
transcriptogramer Diego Morais Transcriptional analysis based on transcriptograms
transcriptR Armen R. Karapetyan An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
transformGamPoi Constantin Ahlmann-Eltze Variance Stabilizing Transformation for Gamma-Poisson Models
transite Konstantin Krismer RNA-binding protein motif analysis
tRanslatome Toma Tebaldi, Erik Dassi Comparison between multiple levels of gene expression
transmogR Stevie Pederson Modify a set of reference sequences using a set of variants
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
traseR li chen GWAS trait-associated SNP enrichment analyses in genomic intervals
traviz Koen Van den Berge Trajectory functions for visualization and interpretation.
TreeAndLeaf Milena A. Cardoso Displaying binary trees with focus on dendrogram leaves
treeclimbR Charlotte Soneson An algorithm to find optimal signal levels in a tree
treeio Guangchuang Yu Base Classes and Functions for Phylogenetic Tree Input and Output
treekoR Adam Chan Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations
TreeSummarizedExperiment Ruizhu Huang TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
TREG Louise Huuki-Myers Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
Trendy Rhonda Bacher Breakpoint analysis of time-course expression data
TRESS Zhenxing Guo Toolbox for mRNA epigenetics sequencing analysis
tricycle Shijie Zheng tricycle: Transferable Representation and Inference of cell cycle
trigger John D. Storey Transcriptional Regulatory Inference from Genetics of Gene ExpRession
trio Holger Schwender Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
triplex Jiri Hon Search and visualize intramolecular triplex-forming sequences in DNA
tripr Nikolaos Pechlivanis T-cell Receptor/Immunoglobulin Profiler (TRIP)
tRNA Felix GM Ernst Analyzing tRNA sequences and structures
tRNAdbImport Felix G.M. Ernst Importing from tRNAdb and mitotRNAdb as GRanges objects
tRNAscanImport Felix G.M. Ernst Importing a tRNAscan-SE result file as GRanges object
TRONCO Luca De Sano TRONCO, an R package for TRanslational ONCOlogy
TSAR Xinlin Gao Thermal Shift Analysis in R
TSCAN Zhicheng Ji Tools for Single-Cell Analysis
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 Dolors Pelegri-Siso RNA-seq data analysis using the Poisson-Tweedie family of distributions
twilight Stefanie Scheid Estimation of local false discovery rate
twoddpcr Anthony Chiu Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules
txcutr Mervin Fansler Transcriptome CUTteR
txdbmaker H. Pagès Tools for making TxDb objects from genomic annotations
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
UCell Massimo Andreatta Rank-based signature enrichment analysis for single-cell data
UCSC.utils Hervé Pagès Low-level utilities to retrieve data from the UCSC Genome Browser
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 Marcel Ramos 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
updateObject Hervé Pagès Find/fix old serialized S4 instances
UPDhmm Marta Sevilla Detecting Uniparental Disomy through NGS trio data
uSORT Hao Chen uSORT: A self-refining ordering pipeline for gene selection
VAExprs Dongmin Jung Generating Samples of Gene Expression Data with Variational Autoencoders
VanillaICE 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 drivers 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
VDJdive Kelly Street Analysis Tools for 10X V(D)J Data
VegaMC Sandro Morganella VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer
velociraptor Kevin Rue-Albrecht Toolkit for Single-Cell Velocity
veloviz Lyla Atta VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories
VennDetail Kai Guo A package for visualization and extract details
VERSO Davide Maspero Viral Evolution ReconStructiOn (VERSO)
vidger Brandon Monier Create rapid visualizations of RNAseq data in R
viper Mariano J Alvarez Virtual Inference of Protein-activity by Enriched Regulon analysis
ViSEAGO Aurelien Brionne ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
VisiumIO Marcel Ramos Import Visium data from the 10X Space Ranger pipeline
vissE Dharmesh D. Bhuva Visualising Set Enrichment Analysis Results
Voyager Lambda Moses From geospatial to spatial omics
VplotR Jacques Serizay Set of tools to make V-plots and compute footprint profiles
vsclust Veit Schwaemmle Feature-based variance-sensitive quantitative clustering
vsn Wolfgang Huber Variance stabilization and calibration for microarray data
vtpnet VJ Carey variant-transcription factor-phenotype networks
vulcan Federico M. Giorgi VirtUaL ChIP-Seq data Analysis using Networks
waddR Julian Flesch Statistical tests for detecting differential distributions based on the 2-Wasserstein distance
wateRmelon Leo C Schalkwyk Illumina 450 and EPIC methylation array normalization and metrics
wavClusteR Federico Comoglio Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
weaver Seth Falcon Tools and extensions for processing Sweave documents
webbioc Colin A. Smith Bioconductor Web Interface
weitrix Paul Harrison Tools for matrices with precision weights, test and explore weighted or sparse data
widgetTools Jianhua Zhang Creates an interactive tcltk widget
wiggleplotr Kaur Alasoo Make read coverage plots from BigWig files
wpm Helene Borges Well Plate Maker
wppi Ana Galhoz Weighting protein-protein interactions
Wrench Hector Corrada Bravo Wrench normalization for sparse count data
xcms Steffen Neumann LC-MS and GC-MS Data Analysis
xcore Maciej Migdał xcore expression regulators inference
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 Zuguang Gu Yet Another Package for Signature Analysis
yarn Joseph N Paulson YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
zellkonverter Luke Zappia Conversion Between scRNA-seq Objects
zenith Gabriel Hoffman Gene set analysis following differential expression using linear (mixed) modeling with dream
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
ZygosityPredictor Marco Rheinnecker Package for prediction of zygosity for variants/genes in NGS data