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Bioconductor Software Packages
Bioconductor version: Release (3.22)
| 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 |
| anansi | Thomaz Bastiaanssen | Annotation-Based Analysis of Specific Interactions |
| 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 |
| anglemania | Aaron Kollotzek | Feature Extraction for scRNA-seq Dataset Integration |
| animalcules | Jessica McClintock | Interactive microbiome analysis toolkit |
| annaffy | Colin A. Smith | Annotation tools for Affymetrix biological metadata |
| anndataR | Robrecht Cannoodt | AnnData interoperability in R |
| 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 |
| AWAggregator | Jiahua Tan | Attribute-Weighted Aggregation |
| 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 |
| batchCorr | Anton Ribbenstedt | Within And Between Batch Correction Of LC-MS Metabolomics Data |
| batchelor | Aaron Lun | Single-Cell Batch Correction Methods |
| BatchQC | Jessica Anderson | Batch Effects Quality Control Software |
| BatchSVG | Kinnary Shah | 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 |
| Bioc.gff | Bioconductor Package Maintainer | Read and write GFF and GTF files |
| 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 | Lluís 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 | Hugo Gruson | 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 |
| blase | Andrew McCluskey | Bulk Linking Analysis for Single-cell Experiments |
| blima | Vojtěch Kulvait | Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level |
| BLMA | Van-Dung Pham | BLMA: A package for bi-level meta-analysis |
| BloodGen3Module | Darawan Rinchai | This R package for performing module repertoire analyses and generating fingerprint representations |
| bluster | Aaron Lun | Clustering Algorithms for Bioconductor |
| bnbc | Kipper Fletez-Brant | Bandwise normalization and batch correction of Hi-C data |
| bnem | Martin Pirkl | Training of logical models from indirect measurements of perturbation experiments |
| BOBaFIT | Gaia Mazzocchetti | Refitting diploid region profiles using a clustering procedure |
| borealis | Garrett Jenkinson | Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution |
| BPRMeth | Chantriolnt-Andreas Kapourani | Model higher-order methylation profiles |
| BRAIN | Piotr Dittwald | Baffling Recursive Algorithm for Isotope distributioN calculations |
| branchpointer | Beth Signal | Prediction of intronic splicing branchpoints |
| breakpointR | David Porubsky | Find breakpoints in Strand-seq data |
| BreastSubtypeR | Qiao Yang | Cohort-aware methods for intrinsic molecular subtyping of breast cancer |
| 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 | Fabrício Almeida-Silva | Candidate Gene Miner |
| CAGEr | Charles Plessy | Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining |
| CalibraCurve | Karin Schork | Calibration curves for targeted proteomics, lipidomics and metabolomics data |
| 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 |
| CBN2Path | William Choi-Kim | "CBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjunctive Bayesian Networks |
| 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 |
| cellmig | Simo Kitanovski | Uncertainty-aware quantitative analysis of high-throughput live cell migration data |
| 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 Lågstad | Visualization tools for gene fusions |
| ChIPanalyser | Patrick C.N. Martin | ChIPanalyser: Predicting Transcription Factor Binding Sites |
| ChIPComp | Li Chen | Quantitative comparison of multiple ChIP-seq datasets |
| chipenrich | Kai Wang | Gene Set Enrichment For ChIP-seq Peak Data |
| ChIPexoQual | Rene Welch | ChIPexoQual |
| ChIPpeakAnno | Jianhong Ou, Lihua Julie Zhu, Kai Hu, Junhui Li | Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data |
| ChIPQC | Tom Carroll, Rory Stark | Quality metrics for ChIPseq data |
| ChIPseeker | Guangchuang Yu | ChIPseeker for ChIP peak Annotation, Comparison, and Visualization |
| chipseq | Bioconductor Package Maintainer | chipseq: A package for analyzing chipseq data |
| ChIPseqR | Peter Humburg | Identifying Protein Binding Sites in High-Throughput Sequencing Data |
| ChIPsim | Peter Humburg | Simulation of ChIP-seq experiments |
| ChIPXpress | George Wu | ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles |
| chopsticks | Hin-Tak Leung | The 'snp.matrix' and 'X.snp.matrix' Classes |
| Chromatograms | Philippine Louail | Infrastructure for Chromatographic Mass Spectrometry Data |
| 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 |
| cigarillo | Hervé Pagès | Efficient manipulation of CIGAR strings |
| 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 | Boris Lenhard Damir Baranasic | 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 | Fabrício Almeida-Silva | Systematic quality checks on comparative genomics analyses |
| Cogito | Annika Bürger | Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets |
| coGPS | Yingying Wei | cancer outlier Gene Profile Sets |
| cola | Zuguang Gu | A Framework for Consensus Partitioning |
| comapr | Ruqian Lyu | Crossover analysis and genetic map construction |
| combi | Stijn Hawinkel | Compositional omics model based visual integration |
| 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 | Anthony B. Crumley | 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 |
| CSOA | Andrei-Florian Stoica | Calculate per-cell gene signature scores in scRNA-seq data using cell set overlaps |
| 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 |
| DeeDeeExperiment | Najla Abassi | DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results |
| 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 Oleś | Differential gene expression data formats converter |
| DegCre | Brian S. Roberts | Probabilistic association of DEGs to CREs from differential data |
| DegNorm | Ji-Ping Wang | DegNorm: degradation normalization for RNA-seq data |
| DEGraph | Laurent Jacob | Two-sample tests on a graph |
| DEGreport | Lorena Pantano | Report of DEG analysis |
| DEGseq | Likun Wang | Identify Differentially Expressed Genes from RNA-seq data |
| DelayedArray | Hervé Pagès | A unified framework for working transparently with on-disk and in-memory array-like datasets |
| DelayedDataFrame | Qian Liu | Delayed operation on DataFrame using standard DataFrame metaphor |
| DelayedMatrixStats | Peter Hickey | Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects |
| DelayedRandomArray | Aaron Lun | Delayed Arrays of Random Values |
| DelayedTensor | Koki Tsuyuzaki | R package for sparse and out-of-core arithmetic and decomposition of Tensor |
| DELocal | Rishi Das Roy | Identifies differentially expressed genes with respect to other local genes |
| deltaCaptureC | Michael Shapiro | This Package Discovers Meso-scale Chromatin Remodeling from 3C Data |
| deltaGseg | Diana Low | deltaGseg |
| DeMAND | Jung Hoon Woo, Mariano Alvarez | DeMAND |
| DeMixT | 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-García | 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 |
| DOtools | Mariano Ruz Jurado | Convenient functions to streamline your single cell data analysis workflow |
| doubletrouble | Fabrício 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 |
| DspikeIn | Mitra Ghotbi | Estimating Absolute Abundance from Microbial Spike-in Controls |
| 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 Oleś | Image processing and analysis toolbox for R |
| EBSEA | Arfa Mehmood | Exon Based Strategy for Expression Analysis of genes |
| EBSeq | Xiuyu Ma | An R package for gene and isoform differential expression analysis of RNA-seq data |
| 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 | Jared Andrews | 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-Díaz | Evaluation of Bioinformatics Metrics |
| EventPointer | Juan A. Ferrer-Bonsoms | An effective identification of alternative splicing events using junction arrays and RNA-Seq data |
| EWCE | Hiranyamaya Dash | 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 | Anil Thanki | 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 |
| FinfoMDS | Soobin Kim | Multidimensional Scaling with F-ratio for microbiome visualization |
| 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 Veríssimo | Network Centrality Metrics for Elastic-Net Regularized Models |
| GlobalAncova | Manuela Hummel | Global test for groups of variables via model comparisons |
| globalSeq | Armin Rauschenberger | Global Test for Counts |
| globaltest | Jelle Goeman | Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing |
| GloScope | Elizabeth Purdom | 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 |
| goatea | Maurits Unkel | Interactive Exploration of GSEA by the GOAT Method |
| 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 |
| gVenn | Christophe Tav | Proportional Venn and UpSet Diagrams for Gene Sets and Genomic Regions |
| 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 |
| HiCaptuRe | Laureano Tomas-Daza | HiCaptuRe: Manipulating and integrating Capture Hi-C data |
| HiCBricks | Koustav Pal | Framework for Storing and Accessing Hi-C Data Through HDF Files |
| HiCcompare | Mikhail Dozmorov | HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets |
| HiCDCPlus | Merve Sahin | Hi-C Direct Caller Plus |
| HiCDOC | Maigné Élise | A/B compartment detection and differential analysis |
| HiCExperiment | Jacques Serizay | Bioconductor class for interacting with Hi-C files in R |
| HiContacts | Jacques Serizay | Analysing cool files in R with HiContacts |
| HiCool | Jacques Serizay | HiCool |
| HiCParser | Maigné Élise | Parser for HiC data in R |
| HiCPotts | Itunu. Godwin Osuntoki | HiCPotts: Hierarchical Modeling to Identify and Correct Genomic Biases in Hi-C |
| 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 | Andrew Chen | 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 |
| Ibex | Nick Borcherding | Methods for BCR single-cell embedding |
| 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 |
| iModMix | Isis Narvaez-Bandera | Integrative Modules for Multi-Omics Data |
| 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 |
| iscream | James Eapen | Make fast and memory efficient BED file queries, summaries and matrices |
| 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 |
| linkSet | Gilbert Han | Base Classes for Storing Genomic Link 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 |
| looking4clusters | David Barrios | Interactive Visualization of scRNA-Seq |
| 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 | Fabrício 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 |
| markeR | Rita Martins-Silva | An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers |
| 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 |
| MetaDICT | Bo Yuan | Microbiome data integration method via shared dictionary learning |
| 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 | Dashboard for the interactive analysis and exploration of microbiome data |
| miaSim | Yagmur Simsek | Microbiome Data Simulation |
| miaTime | Tuomas Borman | Microbiome Time Series Analysis |
| 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 Migdał | R package for immunogenomics data handling and association analysis |
| miloR | Mike Morgan | Differential neighbourhood abundance testing on a graph |
| mimager | Aaron Wolen | mimager: The Microarray Imager |
| mina | Rui Guan | Microbial community dIversity and Network Analysis |
| MineICA | Anne Biton | Analysis of an ICA decomposition obtained on genomics data |
| minet | Patrick E. Meyer | Mutual Information NETworks |
| minfi | Kasper Daniel Hansen | Analyze Illumina Infinium DNA methylation arrays |
| MinimumDistance | Robert Scharpf | A Package for De Novo CNV Detection in Case-Parent Trios |
| MiPP | Sukwoo Kim | Misclassification Penalized Posterior Classification |
| miQC | Ariel Hippen | Flexible, probabilistic metrics for quality control of scRNA-seq data |
| MIRA | John Lawson | Methylation-Based Inference of Regulatory Activity |
| MiRaGE | Y-h. Taguchi | MiRNA Ranking by Gene Expression |
| miRBaseConverter | Taosheng Xu 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-María Novoa-del-Toro | MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks |
| mogsa | Chen Meng | Multiple omics data integrative clustering and gene set analysis |
| MoleculeExperiment | Shila Ghazanfar | Prioritising a molecule-level storage of Spatial Transcriptomics Data |
| MOMA | Sunny Jones | Multi Omic Master Regulator Analysis |
| monaLisa | Michael Stadler | Binned Motif Enrichment Analysis and Visualization |
| monocle | Cole Trapnell | Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq |
| Moonlight2R | Matteo Tiberti | Identify oncogenes and tumor suppressor genes from omics data |
| MoonlightR | Matteo Tiberti | Identify oncogenes and tumor suppressor genes from omics data |
| mosaics | Dongjun Chung | MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq) |
| mosbi | Tim Daniel Rose | Molecular Signature identification using Biclustering |
| 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 |
| MSstatsResponse | Sarah Szvetecz | Statistical Methods for Chemoproteomics Dose-Response Analysis |
| 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 |
| mutscan | Charlotte Soneson | Preprocessing and Analysis of Deep Mutational Scanning Data |
| 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 | Marouen Ben Guebila | A menagerie of 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 |
| notame | Vilhelm Suksi | Workflow for non-targeted LC-MS metabolic profiling |
| notameStats | Vilhelm Suksi | Workflow for non-targeted LC-MS metabolic profiling |
| notameViz | Vilhelm Suksi | Workflow for non-targeted LC-MS metabolic profiling |
| 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 |
| omicsGMF | Alexandre Segers | Dimensionality reduction of (single-cell) omics data in R using omicsGMF |
| 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 |
| peakCombiner | Markus Muckenhuber | The R package to curate and merge enriched genomic regions into consensus peak sets |
| 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 | Di Xiao | 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 | Lucas Etourneau | 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 | Fabrício Almeida-Silva | Identification and classification of plant transcription factors |
| plasmut | Adith Arun | Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic |
| plgem | Norman Pavelka | Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM) |
| plier | Crispin Miller | Implements the Affymetrix PLIER algorithm |
| 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 |
| PMScanR | Jan Pawel Jastrzebski | Protein motifs analysis and visualisation |
| 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 | Nicholas J. Eagles | 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 | Hugo Gruson | Read Zarr Files in R |
| rawDiag | Christian Panse | Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful |
| rawrr | Christian Panse | Direct Access to Orbitrap Data and Beyond |
| RbcBook1 | Vince Carey | Support for Springer monograph on Bioconductor |
| Rbec | Pengfan Zhang | Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities |
| RBGL | Bioconductor Package Maintainer | An interface to the BOOST graph library |
| RBioFormats | Andrzej Oleś | R interface to Bio-Formats |
| 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 | Jing Chen | 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 | Hugo Gruson | R Interface to HDF5 |
| rhdf5client | Alexey Sergushichev | Access HDF5 content from HDF Scalable Data Service |
| rhdf5filters | Hugo Gruson | HDF5 Compression Filters |
| Rhdf5lib | Hugo Gruson | 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-García | 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 |
| SanityR | Teo Sakel | R/Bioconductor interface to the Sanity model gene expression analysis |
| 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 |
| scafari | Sophie Wind | Analysis of scDNA-seq data |
| 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 | Differential Composition and Variability Analysis for Single-Cell Data |
| scDataviz | Kevin Blighe | scDataviz: single cell dataviz and downstream analyses |
| scDblFinder | Pierre-Luc Germain | scDblFinder |
| scDD | Keegan Korthauer | Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions |
| scDDboost | Xiuyu Ma | A compositional model to assess expression changes from single-cell rna-seq data |
| scde | Evan Biederstedt | Single Cell Differential Expression |
| scDesign3 | Dongyuan Song | A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics |
| 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) |
| scGraphVerse | Francesco Cecere | scGraphVerse: A Gene Network Analysis Package |
| 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 |
| scLANE | Jack R. Leary | Model Gene Expression Dynamics with Spline-Based NB GLMs, GEEs, & GLMMs |
| 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 |
| SETA | Kyle Kimler | Single Cell Ecological Taxonomic Analysis |
| 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 |
| shinybiocloader | Marcel Ramos | Use a Shiny Bioconductor CSS loader |
| shinyDSP | Seung J. Kim | A Shiny App For Visualizing Nanostring GeoMx DSP Data |
| shinyepico | Octavio Morante-Palacios | ShinyÉPICo |
| shinyMethyl | Jean-Philippe Fortin | Interactive visualization for Illumina methylation arrays |
| ShortRead | Bioconductor Package Maintainer | FASTQ input and manipulation |
| SIAMCAT | Jakob Wirbel | Statistical Inference of Associations between Microbial Communities And host phenoTypes |
| SICtools | Xiaobin Xing | Find SNV/Indel differences between two bam files with near relationship |
| SigCheck | Rory Stark | Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata |
| sigFeature | Pijush Das Developer | sigFeature: Significant feature selection using SVM-RFE & t-statistic |
| SigFuge | Patrick Kimes | SigFuge |
| siggenes | Holger Schwender | Multiple Testing using SAM and Efron's Empirical Bayes Approaches |
| sights | Elika Garg | Statistics and dIagnostic Graphs for HTS |
| signatureSearch | Brendan Gongol | Environment for Gene Expression Searching Combined with Functional Enrichment Analysis |
| signeR | Renan Valieris | Empirical Bayesian approach to mutational signature discovery |
| signifinder | Stefania Pirrotta | Collection and implementation of public transcriptional cancer signatures |
| SigsPack | Franziska Schumann | Mutational Signature Estimation for Single Samples |
| sigsquared | UnJin Lee | Gene signature generation for functionally validated signaling pathways |
| SIM | Renee X. de Menezes | Integrated Analysis on two human genomic datasets |
| SIMAT | M. R. Nezami Ranjbar | GC-SIM-MS data processing and alaysis tool |
| 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 | Jean-Philippe Villemin | Cell Signalling Using Single-Cell RNA-seq or Proteomics Data |
| 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 |
| SmartPhos | Shubham Agrawal | A phosphoproteomics data analysis package with an interactive ShinyApp |
| 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 |
| SpaceTrooper | Dario Righelli | SpaceTrooper performs Quality Control analysis of Image-Based spatial |
| 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 |
| spARI | Yinqiao Yan | Spatially Aware Adjusted Rand Index for Evaluating Spatial Transcritpomics Clustering |
| 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 |
| SPICEY | Georgina Fuentes-Páez | Calculates cell type specificity from single cell data |
| 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 |
| STADyUM | Rebecca Hassett | Statistical Transcriptome Analysis under a Dynamic Unified Model |
| 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 |
| stPipe | Yang Xu | Upstream pre-processing for Sequencing-Based Spatial Transcriptomics |
| 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 |
| SuperCellCyto | Givanna Putri | SuperCell For Cytometry 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 Comparative Genomics |
| synlet | Chunxuan Shao | Hits Selection for Synthetic Lethal RNAi Screen Data |
| SynMut | Haogao Gu | SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures |
| syntenet | Fabrício Almeida-Silva | Inference And Analysis Of Synteny Networks |
| systemPipeR | Thomas Girke | systemPipeR: Workflow 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 | Kiloni Quiles | 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 | Yosra Berrouayel | TFEA.ChIP, a Tool Kit for 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 | Federico Marini | 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 Migdał | 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 | Daniel Huebschmann | Yet Another Package for Signature Analysis |
| yarn | Joseph N Paulson | YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization |
| zellkonverter | Luke Zappia | Conversion Between scRNA-seq Objects |
| 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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