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Bioconductor - 3.22 Software Packages
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 ADAPT Mukai Wang Analysis of Microbiome Differential Abundance by Pooling Tobit Models 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 classifier 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 alabaster.se Aaron Lun Load and Save SummarizedExperiments from File alabaster.sfe Lambda Moses Language agnostic on disk serialization of SpatialFeatureExperiment 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 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 AnVILAz Marcel Ramos R / Bioconductor Support for the AnVIL Azure Platform AnVILBase Marcel Ramos Generic functions for interacting with the AnVIL ecosystem AnVILBilling Vince Carey Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org). AnVILGCP Marcel Ramos The GCP R Client for the 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) assorthead Aaron Lun Assorted Header-Only C++ Libraries ASURAT Keita Iida Functional annotation-driven unsupervised clustering for single-cell data 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 Statistical 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 barbieQ Liyang Fei Analyze Barcode Data from Clonal Tracking Experiments 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 Centralized Conda Installation for Bioconductor Packages batchelor Aaron Lun Single-Cell Batch Correction Methods BatchQC Jessica Anderson Batch Effects Quality Control Software BatchSVG Christine Hou Identify Batch-Biased Features in Spatially Variable Genes BayesKnockdown William Chad Young BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data BayesSpace Senbai Kang 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 beachmat Aaron Lun Compiling Bioconductor to Handle Each Matrix Type beachmat.hdf5 Aaron Lun beachmat bindings for HDF5-backed matrices beachmat.tiledb Aaron Lun beachmat bindings for TileDB-backed matrices beadarray Mark Dunning Quality assessment and low-level analysis for Illumina BeadArray data BeadDataPackR Mike Smith Compression of Illumina BeadArray data BEAT Kemal Akman BEAT - BS-Seq Epimutation Analysis Toolkit BEclear Livia Rasp Correction of batch effects in DNA methylation data bedbaser Andres Wokaty A BEDbase client beer Athena Chen Bayesian Enrichment Estimation in R benchdamic Matteo Calgaro Benchmark of differential abundance methods on microbiome data BERT Yannis Schumann High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batch-Effect Reduction Trees (BERT) 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 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 Thomas Girke 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 biocmake Aaron Lun CMake for Bioconductor BiocNeighbors Aaron Lun Nearest Neighbor Detection for Bioconductor Packages BioCor LluÃs Revilla Sancho Functional similarities BiocParallel Jiefei Wang 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 Maintainer Standard styles for vignettes and other Bioconductor documents biocthis Leonardo Collado-Torres Automate package and project setup for Bioconductor packages BiocVersion Bioconductor Package Maintainer Set the appropriate version of Bioconductor packages biocViews Bioconductor Package Maintainer Categorized views of R package repositories BiocWorkflowTools Mike Smith Tools to aid the development of Bioconductor Workflow packages biodb Pierrick Roger Biodb, a Library and a Development Framework for Connecting to Chemical and Biological Databases biodbChebi Pierrick Roger biodbChebi, a library for connecting to the ChEBI Database biodbHmdb Pierrick Roger biodbHmdb, a library for connecting to the HMDB Database 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 BioGA Dany Mukesha Bioinformatics Genetic Algorithm (BioGA) 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 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 Felix Yu 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 VojtÄch 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 branchpointer Beth Signal Prediction of intronic splicing branchpoints breakpointR David Porubsky Find breakpoints in Strand-seq data BreastSubtypeR Qiao Yang Methods for breast cancer intrinsic subtyping brendaDb Yi Zhou The BRENDA Enzyme Database BREW3R.r Lucille Lopez-Delisle R package associated to BREW3R BridgeDbR Egon Willighagen Code for using BridgeDb identifier mapping framework from within R broadSeq Rishi Das Roy broadSeq : for streamlined exploration of RNA-seq data 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 your own BSgenome data package bsseq Kasper Daniel Hansen Analyze, manage and store whole-genome methylation 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 BulkSignalR Jean-Philippe Villemin Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics 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 FabrÃcio 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 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 CARDspa Jing Fu Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics 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 CatsCradle Michael Shapiro This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters CausalR Glyn Bradley, Steven Barrett Causal network analysis methods cbaf Arman Shahrisa Automated functions for comparing various omic data from cbioportal.org cBioPortalData Marcel Ramos Exposes and Makes Available Data from the cBioPortal Web Resources 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 CCAFE Hayley Wolff Case Control Allele Frequency Estimation 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 (https://doi.org/10.1186/s12859-022-04814-8) 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 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 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 chevreulPlot Kevin Stachelek Plots used in the chevreulPlot package chevreulProcess Kevin Stachelek Tools for managing SingleCellExperiment objects as projects chevreulShiny Kevin Stachelek Tools for managing SingleCellExperiment objects as projects Chicago Mikhail Spivakov CHiCAGO: Capture Hi-C Analysis of Genomic Organization chihaya Aaron Lun Save Delayed Operations to a HDF5 File chimeraviz Stian LÃ¥gstad 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 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 End-to-End Analysis of Small RNA-Seq Data from Viroids 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 CleanUpRNAseq Haibo Liu Detect and Correct Genomic DNA Contamination in RNA-seq 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 robustly identify stratification 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 Rui Fu Classifier for Single-cell RNA-seq Using Cell Clusters ClustIRR Simo Kitanovski Clustering of immune receptor repertoires clustSIGNAL Pratibha Panwar ClustSIGNAL: a spatial clustering method 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 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 FabrÃcio 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 coMethDMR Fernanda Veitzman Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies 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 Identify Spatial Homogeneous Regions with concordex 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 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 Coralysis António Sousa Coralysis sensitive identification of imbalanced cell types and states in single-cell data via multi-level integration coRdon Anamaria Elek Codon Usage Analysis and Prediction of Gene Expressivity 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 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 CPSM Harpreet Kaur CPSM: Cancer patient survival model 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 Kai Hu Design of guide RNAs in CRISPR genome-editing systems 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 crumblr Gabriel Hoffman Count ratio uncertainty modeling base linear regression crupR Persia Akbari Omgba An R package to predict condition-specific enhancers from ChIP-seq 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 dandelionR Kelvin Tuong Single-cell Immune Repertoire Trajectory Analysis in R 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 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 Joshua Campbell Decontamination of single cell genomics data DeconvoBuddies Louise Huuki-Myers Helper Functions for LIBD Deconvolution 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. DeepTarget Trinh Nguyen Deep characterization of cancer drugs DEFormats Andrzej OleÅ 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 Ruonan Li 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 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 and differential spatial patterns across conditions 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-GarcÃa Differential Expression Meta-Analysis DEXSeq Alejandro Reyes Inference of differential exon usage in RNA-Seq DFP Rodrigo Alvarez-Glez Gene Selection DFplyr Jonathan Carroll A `DataFrame` (`S4Vectors`) backend for `dplyr` 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 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 dmGsea Zongli Xu Efficient Gene Set Enrichment Analysis for DNA Methylation Data 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 DNAcycP2 Ji-Ping Wang DNA Cyclizability Prediction DNAfusion Christoffer Trier Maansson Identification of gene fusions using paired-end sequencing DNAshapeR Tsu-Pei Chiu High-throughput prediction of DNA shape features DNEA Christopher Patsalis Differential Network Enrichment Analysis for Biological Data DominoEffect Marija Buljan, Peter Blattmann Identification and Annotation of Protein Hotspot Residues dominoSignal Jacob T Mitchell Cell Communication Analysis for Single Cell RNA Sequencing 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 FabrÃcio Almeida-Silva Identification and classification of duplicated genes 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 DuplexDiscovereR Egor Semenchenko Analysis of the data from RNA duplex probing experiments 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 OleÅ 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 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 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 ELViS Jin-Young Lee An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile 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 EnrichDO Hongyu Fu a Global Weighted Model for Disease Ontology Enrichment Analysis 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 enrichViewNet Astrid Deschênes From functional enrichment results to biological networks ensembldb Johannes Rainer Utilities to create and use Ensembl-based annotation databases epialleleR Oleksii Nikolaienko Fast, Epiallele-Aware Methylation Caller and Reporter EpiCompare Hiranyamaya Dash 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 EpipwR Jackson Barth Efficient Power Analysis for EWAS with Continuous or Binary Outcomes 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 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-DÃaz 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 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 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 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 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 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 funOmics Elisa Gomez de Lope Aggregating Omics Data into Higher-Level Functional Representations funtooNorm Kathleen Klein Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit FuseSOM Elijah Willie A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets G4SNVHunter Rongxin Zhang Evaluating SNV-Induced Disruption of G-Quadruplex Structures 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 GCPtools Marcel Ramos Tools for working with gcloud and gsutil 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 Xiuwen Zheng 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 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 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 Query the gene models of a given organism/assembly 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 geomeTriD Jianhong Ou A R/Bioconductor package for interactive 3D plot of epigenetic data or single cell data 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) getDEE2 Mark 0000-0002-7688-6974 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 geyser David McGaughey Gene Expression displaYer of SummarizedExperiment in R 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 Analyzing and visualizing KEGG information using the grammar of graphics ggmanh John Lee Visualization Tool for GWAS Result ggmsa Guangchuang Yu 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 ggseqalign Simeon Lim Rossmann Minimal Visualization of Sequence Alignments 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 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 VerÃssimo 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 Federico Marini Gene Ontology analyser for RNA-seq and other length biased data 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 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 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 h5mread Hervé Pagès A fast HDF5 reader 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 datasets as array-like objects in R 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 Ãlise 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 HiCParser Maigné Ãlise Parser for HiC data in R 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 HoloFoodR Tuomas Borman R interface to EBI HoloFood resource 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 Matthew N. McCall Automated analysis of high-throughput qPCR data HTSFilter Andrea Rau Filter replicated high-throughput transcriptome sequencing data HuBMAPR Christine Hou Interface to 'HuBMAP' HubPub Kayla Interdonato Utilities to create and use Bioconductor Hubs hummingbird Eleni Adam Bayesian Hidden Markov Model for the detection of differentially methylated regions HVP Wei Xin Chan Hierarchical Variance Partitioning 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 Parichoy Pal Choudhury 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 igblastr Hervé Pagès User-friendly R Wrapper to IgBLAST 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 imageTCGA Ilaria Billato TCGA Diagnostic Image Database Explorer 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 immApex Nick Borcherding Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning immunoClust Till Soerensen immunoClust - Automated Pipeline for Population Detection in Flow Cytometry immunogenViewer Katharina Waury Visualization and evaluation of protein immunogens 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 Intron-Exon Retention Estimator IntramiRExploreR Surajit Bhattacharya Predicting Targets for Drosophila Intragenic miRNAs IONiseR Mike Smith Quality Assessment Tools for Oxford Nanopore MinION data 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 ISAnalytics Francesco Gazzo 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 iSEEtree Giulio Benedetti Interactive visualisation for microbiome data 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 islify Jakob Theorell Automatic scoring and classification of cell-based assay images 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 ITALICS Guillem Rigaill ITALICS iterativeBMA Ka Yee Yeung The Iterative Bayesian Model Averaging (BMA) algorithm iterativeBMAsurv Ka Yee Yeung The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis IVAS Seonggyun Han Identification of genetic Variants affecting Alternative Splicing ivygapSE VJ Carey A SummarizedExperiment for Ivy-GAP data IWTomics Marzia A Cremona Interval-Wise Testing for Omics Data jazzPanda Melody Jin Finding spatially relevant marker genes in image based spatial transcriptomics 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 kmcut Igor Kuznetsov Optimized Kaplan Meier analysis and identification and validation of prognostic biomarkers KnowSeq Daniel Castillo-Secilla KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline knowYourCG Goldberg David Functional analysis of DNA methylome datasets koinar Ludwig Lautenbacher KoinaR - Remote machine learning inference using Koina 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 LEA: an R package for Landscape and Ecological Association Studies LedPred Aitor Gonzalez Learning from DNA to Predict Enhancers lefser Sehyun Oh 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 Lheuristic Sanchez Pla Alex Detection of scatterplots with L-shaped pattern limma Gordon Smyth Linear Models for Microarray and Omics Data limmaGUI Gordon Smyth GUI for limma Package With Two Color Microarrays limpa Gordon Smyth Quantification and Differential Analysis of Proteomics Data limpca Manon Martin An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family of methods LimROTS Ali Mostafa Anwar LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis 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 LipidTrend Wei-Chung Cheng LipidTrend: Analysis and Visualization of Lipid Feature Tendencies 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" maaslin3 William Nickols "Refining and extending generalized multivariate linear models for meta-omic association discovery" 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 magpie Daoyu Duan MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation magrene FabrÃcio Almeida-Silva Motif Analysis In Gene Regulatory Networks MAI Jonathan Dekermanjian Mechanism-Aware Imputation 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 Out-of-core statistical computing and signal processing 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 MetaboDynamics Katja Danielzik Bayesian analysis of longitudinal 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 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 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 Bacher Rhonda Visualization of Methylation Data MethylSeekR Lukas Burger Segmentation of Bis-seq data methylSig Raymond G. Cavalcante MethylSig: Differential Methylation Testing for WGBS and RRBS Data methylumi Sean Davis Handle Illumina methylation data MetID Zhenzhi Li Network-based prioritization of putative metabolite IDs MetMashR Gavin Rhys Lloyd Metabolite Mashing with R 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 omics time series 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 miaDash Giulio Benedetti Shiny app for the interactive analysis and exploration of microbiome data 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 MicrobiomeProfiler Guangchuang Yu 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 "Michael Lawrence" 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 MigdaÅ 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 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 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, Calandra Grima Analysing Illumina HumanMethylation BeadChip Data missRows Gonzalez Ignacio Handling Missing Individuals in Multi-Omics Data Integration mist Daoyu Duan Differential Methylation Analysis for scDNAm Data 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 mitology Stefania Pirrotta Study of mitochondrial activity from RNA-seq data mixOmics Eva Hamrud 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 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 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-MarÃa 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 MOSClip Paolo Martini Multi Omics Survival Clip 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 MotifPeeker Hiranyamaya Dash Benchmarking Epigenomic Profiling Methods Using Motif Enrichment 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 MPAC Peng Liu Multi-omic Pathway Analysis of Cells 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 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 MsBackendMetaboLights Johannes Rainer Retrieve Mass Spectrometry Data from MetaboLights 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 mspms Charlie Bayne Tools for the analysis of MSP-MS data 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 MSstatsBioNet Anthony Wu Network Analysis for MS-based Proteomics Experiments MSstatsConvert Mateusz Staniak Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format MSstatsLiP Anthony Wu 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 Anthony Wu 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 Anthony Wu 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 Ilia Kats 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 Spencer Mahaffey Integration of multiple microRNA-target databases with their disease and drug associations MultimodalExperiment Lucas Schiffer Integrative Bulk and Single-Cell Experiment Container 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 MyVariant.info 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 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 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 nethet Nicolas Staedler, Frank Dondelinger A bioconductor package for high-dimensional exploration of biological network heterogeneity NetPathMiner Ahmed Mohamed NetPathMiner for Biological Network Construction, Path Mining and Visualization netprioR Fabian Schmich A model for network-based prioritisation of genes netresponse Leo Lahti Functional Network Analysis NetSAM Zhiao Shi Network Seriation And Modularization netSmooth Jonathan Ronen Network smoothing for scRNAseq netZooR Tara Eicher Unified methods for the inference and analysis of gene regulatory networks 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 OmicsMLRepoR Sehyun Oh Search harmonized metadata created under the OmicsMLRepo project 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 omXplore Samuel Wieczorek Vizualization tools for 'omics' datasets with R 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 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 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 OSTA.data Yixing E. Dong OSTA book data 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 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 pathMED Jordi Martorell-Marugán Scoring Personalized Molecular Portraits 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 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 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 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 Nezet Pedigree Functions pengls Stijn Hawinkel Fit Penalised Generalised Least Squares models PepSetTest Junmin Wang Peptide Set Test 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. 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 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 piano Leif Varemo Wigge Platform for integrative analysis of omics data PICB Franziska Ahrend piRNA Cluster Builder pickgene Brian S. Yandell Adaptive Gene Picking for Microarray Expression Data Analysis Pigengene Habil Zare Infers biological signatures from gene expression 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 Pirat Samuel Wieczorek Precursor or Peptide Imputation under Random Truncation PIUMA Mattia Chiesa Phenotypes Identification Using Mapper from topological data Analysis planet Victor Yuan Placental DNA methylation analysis tools planttfhunter FabrÃcio 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 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 plyxp Justin Landis Data masks for SummarizedExperiment enabling dplyr-like manipulation 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 poem Siyuan Luo POpulation-based Evaluation Metrics pogos VJ Carey PharmacOGenomics Ontology Support PolySTest Veit Schwämmle PolySTest: Detection of differentially regulated features. Combined statistical testing for data with few replicates and missing values Polytect Yao Chen An R package for digital data clustering 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 Lisa Breckels 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 PRONE Lis Arend The PROteomics Normalization Evaluator PROPER Hao Wu PROspective Power Evaluation for RNAseq PROPS Lichy Han PRObabilistic Pathway Score (PROPS) Prostar Samuel Wieczorek Provides a GUI for DAPAR proteinProfiles Julian Gehring Protein Profiling ProteoDisco Job van Riet Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences 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 psichomics Nuno Saraiva-Agostinho Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation PSMatch Laurent Gatto Handling and Managing Peptide Spectrum Matches 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 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 QRscore Fanding Zhou Quantile Rank Score 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 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 Robust Ancestry Inference using Data Synthesis 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 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 OleÅ R interface to Bio-Formats 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 RbowtieCuda Franck RICHARD An R Wrapper for nvBowtie and nvBWT, a rewritten version of Bowtie2 for cuda 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 Rdisop Steffen Neumann Decomposition of Isotopic Patterns RDRToolbox Christoph Bartenhagen A package for nonlinear dimension reduction with Isomap and LLE. 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 ReducedExperiment Jack Gisby Containers and tools for dimensionally-reduced -omics representations 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 regional cell type-specific 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 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 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). RFLOMICS Nadia Bessoltane Interactive web application for Omics-data analysis 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 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 rhinotypeR Martha Luka Rhinovirus genotyping 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. Rigraphlib Aaron Lun igraph library as an R package rigvf Michael Love R interface to the IGVF Catalog RImmPort Zicheng Hu, Ravi Shankar RImmPort: Enabling Ready-for-analysis Immunology Research Data RITAN Michael Zimmermann Rapid Integration of Term Annotation and Network resources RIVER Yungil Kim R package for RIVER (RNA-Informed Variant Effect on Regulation) RJMCMCNucleosomes Astrid Deschênes Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq) RLassoCox Wei Liu A reweighted Lasso-Cox by integrating gene interaction information RLMM Nusrat Rabbee A Genotype Calling Algorithm for Affymetrix SNP Arrays Rmagpie Camille Maumet MicroArray Gene-expression-based Program In Error rate estimation RMassBank RMassBank at Eawag Workflow to process tandem MS files and build MassBank records rmelting J. Aravind R Interface to MELTING 5 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 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 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 Camila P Perico Spaced Words Projection (SWeeP) 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 rTRM Diego Diez Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks rTRMui Diego Diez A shiny user interface for rTRM RUCova Rosario Astaburuaga-GarcÃa Removes unwanted covariance from mass cytometry data 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 Tests differences in cell-type proportion for single-cell data, robust to outliers 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 scDiagnostics Anthony Christidis Cell type annotation diagnostics scDotPlot Benjamin I Laufer Cluster a Single-cell RNA-seq Dot Plot 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 scHiCcompare My Nguyen Differential Analysis of Single-cell Hi-C 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 Li 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 scoup Hassan Sadiq Simulate Codons with Darwinian Selection Modelled as an OU Process 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 scQTLtools Xiaofeng Wu scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of single-cell eQTLs scran Aaron Lun Methods for Single-Cell RNA-Seq Data Analysis scrapper Aaron Lun Bindings to C++ Libraries for Single-Cell 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 seahtrue Vincent de Boer Seahtrue revives XF data for structured data analysis 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 using GDS files 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 Seqinfo Hervé Pagès A simple S4 class for storing basic information about a collection of genomic sequences 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 SEraster Gohta Aihara Rasterization Preprocessing Framework for Scalable Spatial Omics Data Analysis 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 shinyDSP Seung J. Kim A Shiny App For Visualizing Nanostring GeoMx DSP Data shinyepico Octavio Morante-Palacios ShinyÃPICo 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 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 on Bio-Ontologies simPIC Sagrika Chugh 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 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 Site2Target Peyman Zarrineh An R package to associate peaks and target genes 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) 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 smoppix Stijn Hawinkel Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index 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 sosta Samuel Gunz A package for the analysis of anatomical tissue structures in spatial omics data SpaceMarkers Atul Deshpande Spatial Interaction Markers spacexr Gabriel Grajeda SpatialeXpressionR: Cell Type Identification in Spatial Transcriptomics Spaniel Rachel Queen Spatial Transcriptomics Analysis SpaNorm Dharmesh D. Bhuva Spatially-aware normalisation for spatial transcriptomics data 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 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 SpatialExperimentIO Yixing E. Dong Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object spatialFDA Martin Emons A Tool for Spatial Multi-sample Comparisons SpatialFeatureExperiment Lambda Moses Integrating SpatialExperiment with Simple Features in sf spatialHeatmap Jianhai Zhang spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions SpatialOmicsOverlay Maddy Griswold Spatial Overlay for Omic Data from Nanostring GeoMx Data spatialSimGP Kinnary Shah Simulate Spatial Transcriptomics Data with the Mean-variance Relationship 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 SpectraQL Johannes Rainer MassQL support for Spectra SpectriPy Johannes Rainer Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python 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 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 SplineDV Shreyan Gupta Differential Variability (DV) analysis for single-cell RNA sequencing data. (e.g. Identify Differentially Variable Genes across two experimental conditions) 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 squallms William Kumler Speedy quality assurance via lasso labeling for LC-MS data sRACIPE Mingyang Lu 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 StabMap Shila Ghazanfar Stabilised mosaic single cell data integration using unshared features 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 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 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 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 SummarizedExperiment Hervé Pagès A container (S4 class) for matrix-like assays Summix Audrey Hendricks Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data supersigs Albert Kuo Supervised mutational signatures surfaltr Pooja Gangras Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr SurfR Aurora Maurizio Surface Protein Prediction and Identification survClust Arshi Arora Identification Of Clinically Relevant Genomic Subtypes Using Outcome Weighted Learning 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 SVP Shuangbin Xu Predicting cell states and their variability in single-cell or spatial omics data 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 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 FabrÃcio Almeida-Silva Inference And Analysis Of Synteny Networks systemPipeR Thomas Girke systemPipeR: Workflow Environment for Data Analysis and Report Generation 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 TaxSEA Feargal Ryan Taxon Set Enrichment Analysis 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 TENET Rhie Lab at the University of Southern California R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key transcription factors 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 terapadog Gionmattia Carancini Translational Efficiency Regulation Analysis using the PADOG Method 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 SantamarÃa 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 tidyFlowCore Timothy Keyes tidyFlowCore: Bringing flowCore to the tidyverse tidyomics Stefano Mangiola Easily install and load the tidyomics ecosystem tidysbml Veronica Paparozzi Extract SBML's data into dataframes tidySingleCellExperiment Stefano Mangiola Brings SingleCellExperiment to the Tidyverse tidySpatialExperiment William Hutchison SpatialExperiment with tidy principles tidySummarizedExperiment Stefano Mangiola Brings SummarizedExperiment to the Tidyverse tidytof Timothy Keyes Analyze High-dimensional Cytometry Data Using Tidy Data Principles 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 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 TMSig Tyler Sagendorf Tools for Molecular Signatures 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 TrIdent Jessie Maier TrIdent - Transduction Identification 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 Senger 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 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 UniProt.ws 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 Comprehensive Visualization and Analysis of Multi-Set Intersections 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 visiumStitched Nicholas J. Eagles Enable downstream analysis of Visium capture areas stitched together with Fiji vissE Dharmesh D. Bhuva Visualising Set Enrichment Analysis Results vmrseq Ning Shen Probabilistic Modeling of Single-cell Methylation Heterogeneity Voyager Lambda Moses From geospatial to spatial omics VplotR Jacques Serizay Set of tools to make V-plots and compute footprint profiles vsclust Veit Schwammle 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 DNA 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 XAItest Ghislain FIEVET XAItest: Enhancing Feature Discovery with eXplainable AI xCell2 Almog Angel A Tool for Generic Cell Type Enrichment Analysis xcms Steffen Neumann LC-MS and GC-MS Data Analysis xcore Maciej MigdaÅ xcore expression regulators inference XDE Robert Scharpf XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression XeniumIO Marcel Ramos Import and represent Xenium data from the 10X Xenium Analyzer xenLite Vincent Carey Simple classes and methods for managing Xenium datasets 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 zitools Carlotta Meyring Analysis of zero-inflated count data ZygosityPredictor Marco Rheinnecker Package for prediction of zygosity for variants/genes in NGS data
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