Bioconductor - 3.20 Workflow Packages

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href="/packages/3.19/BiocViews.html#___Software">3.19 (4.4)</a> </div> <div> <a href="/packages/3.18/BiocViews.html#___Software">3.18 (4.3)</a> </div> <div> <a href="/packages/3.17/BiocViews.html#___Software">3.17 (4.3)</a> </div> <div> <a href="/packages/3.16/BiocViews.html#___Software">3.16 (4.2)</a> </div> <div> <a href="/packages/3.15/BiocViews.html#___Software">3.15 (4.2)</a> </div> <div> <a href="/packages/3.14/BiocViews.html#___Software">3.14 (4.1)</a> </div> <div> <a href="/packages/3.13/BiocViews.html#___Software">3.13 (4.1)</a> </div> <div> <a href="/packages/3.12/BiocViews.html#___Software">3.12 (4.0)</a> </div> <div> <a href="/packages/3.11/BiocViews.html#___Software">3.11 (4.0)</a> </div> <div> <a href="/packages/3.10/BiocViews.html#___Software">3.10 (3.6)</a> </div> <div> <a href="/packages/3.9/BiocViews.html#___Software">3.9 (3.6)</a> </div> <div> <a href="/packages/3.8/BiocViews.html#___Software">3.8 (3.5)</a> </div> <div> <a href="/packages/3.7/BiocViews.html#___Software">3.7 (3.5)</a> </div> </nav> <div class="bottom-note"> <p class="text-small"> Release <a href="/about/release-announcements/#release-announcements" >announcements</a >. </p> </div> </div> </div> </section> <section class="content"> <ul class="breadcrumbs"> <li><a href="/">Home</a></li> <li><a href="/packages/3.20/BiocViews.html">Bioconductor 3.20</a></li> <li>3.20 Workflow Packages</li> </ul> <h1>Bioconductor Workflow Packages</h1> <p> Bioconductor version: Release (3.20) </p> <div class="do_not_rebase"> <table> <tr> <th>Package</th> <th>Maintainer</th> <th>Title</th> </tr> <tr class="row_odd"> <td><a href="html/annotation.html">annotation</a></td> <td>Bioconductor Package Maintainer </td> <td>Genomic Annotation Resources</td> </tr> <tr class="row_even"> <td><a href="html/arrays.html">arrays</a></td> <td>Bioconductor Package Maintainer </td> <td>Using Bioconductor for Microarray Analysis</td> </tr> <tr class="row_odd"> <td><a href="html/BiocMetaWorkflow.html">BiocMetaWorkflow</a></td> <td>Mike Smith </td> <td>BioC Workflow about publishing a Bioc Workflow</td> </tr> <tr class="row_even"> <td><a href="html/BP4RNAseq.html">BP4RNAseq</a></td> <td>Shanwen Sun </td> <td>A babysitter's package for reproducible RNA-seq analysis</td> </tr> <tr class="row_odd"> <td><a href="html/CAGEWorkflow.html">CAGEWorkflow</a></td> <td>Malte Thodberg </td> <td>A step-by-step guide to analyzing CAGE data using R/Bioconductor</td> </tr> <tr class="row_even"> <td><a href="html/chipseqDB.html">chipseqDB</a></td> <td>Aaron Lun </td> <td>A Bioconductor Workflow to Detect Differential Binding in ChIP-seq Data</td> </tr> <tr class="row_odd"> <td><a href="html/csawUsersGuide.html">csawUsersGuide</a></td> <td>Aaron Lun </td> <td>csaw User's Guide</td> </tr> <tr class="row_even"> <td><a href="html/cytofWorkflow.html">cytofWorkflow</a></td> <td>Mark D. Robinson </td> <td>CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets</td> </tr> <tr class="row_odd"> <td><a href="html/EGSEA123.html">EGSEA123</a></td> <td>Matthew Ritchie </td> <td>Easy and efficient ensemble gene set testing with EGSEA</td> </tr> <tr class="row_even"> <td><a href="html/ExpHunterSuite.html">ExpHunterSuite</a></td> <td>James Perkins </td> <td>Package For The Comprehensive Analysis Of Transcriptomic Data</td> </tr> <tr class="row_odd"> <td><a href="html/ExpressionNormalizationWorkflow.html">ExpressionNormalizationWorkflow</a></td> <td>Karthikeyan Murugesan </td> <td>Gene Expression Normalization Workflow</td> </tr> <tr class="row_even"> <td><a href="html/fluentGenomics.html">fluentGenomics</a></td> <td>Stuart Lee </td> <td>A plyranges and tximeta workflow</td> </tr> <tr class="row_odd"> <td><a href="html/generegulation.html">generegulation</a></td> <td>Bioconductor Package Maintainer </td> <td>Finding Candidate Binding Sites for Known Transcription Factors via Sequence Matching</td> </tr> <tr class="row_even"> <td><a href="html/GeoMxWorkflows.html">GeoMxWorkflows</a></td> <td>Maddy Griswold </td> <td>GeoMx Digital Spatial Profiler (DSP) data analysis workflows</td> </tr> <tr class="row_odd"> <td><a href="html/highthroughputassays.html">highthroughputassays</a></td> <td>Bioconductor Package Maintainer </td> <td>Using Bioconductor with High Throughput Assays</td> </tr> <tr class="row_even"> <td><a href="html/liftOver.html">liftOver</a></td> <td>Bioconductor Package Maintainer </td> <td>Changing genomic coordinate systems with rtracklayer::liftOver</td> </tr> <tr class="row_odd"> <td><a href="html/maEndToEnd.html">maEndToEnd</a></td> <td>Stefanie Reisenauer </td> <td>An end to end workflow for differential gene expression using Affymetrix microarrays</td> </tr> <tr class="row_even"> <td><a href="html/methylationArrayAnalysis.html">methylationArrayAnalysis</a></td> <td>Jovana Maksimovic </td> <td>A cross-package Bioconductor workflow for analysing methylation array data.</td> </tr> <tr class="row_odd"> <td><a href="html/recountWorkflow.html">recountWorkflow</a></td> <td>Leonardo Collado-Torres </td> <td>recount workflow: accessing over 70,000 human RNA-seq samples with Bioconductor</td> </tr> <tr class="row_even"> <td><a href="html/RNAseq123.html">RNAseq123</a></td> <td>Matthew Ritchie </td> <td>RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR</td> </tr> <tr class="row_odd"> <td><a href="html/rnaseqDTU.html">rnaseqDTU</a></td> <td>Michael Love </td> <td>RNA-seq workflow for differential transcript usage following Salmon quantification</td> </tr> <tr class="row_even"> <td><a href="html/rnaseqGene.html">rnaseqGene</a></td> <td>Michael Love </td> <td>RNA-seq workflow: gene-level exploratory analysis and differential expression</td> </tr> <tr class="row_odd"> <td><a href="html/RnaSeqGeneEdgeRQL.html">RnaSeqGeneEdgeRQL</a></td> <td>Yunshun Chen </td> <td>Gene-level RNA-seq differential expression and pathway analysis using Rsubread and the edgeR quasi-likelihood pipeline</td> </tr> <tr class="row_even"> <td><a href="html/seqpac.html">seqpac</a></td> <td>Daniel Natt </td> <td>Seqpac: A Framework for smallRNA analysis in R using Sequence-Based Counts</td> </tr> <tr class="row_odd"> <td><a href="html/sequencing.html">sequencing</a></td> <td>Bioconductor Package Maintainer </td> <td>Introduction to Bioconductor for Sequence Data</td> </tr> <tr class="row_even"> <td><a href="html/simpleSingleCell.html">simpleSingleCell</a></td> <td>Aaron Lun </td> <td>A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor</td> </tr> <tr class="row_odd"> <td><a href="html/SingscoreAMLMutations.html">SingscoreAMLMutations</a></td> <td>Dharmesh D. Bhuva </td> <td>Using singscore to predict mutations in AML from transcriptomic signatures</td> </tr> <tr class="row_even"> <td><a href="html/spicyWorkflow.html">spicyWorkflow</a></td> <td>SOMS Maintainer </td> <td>Performing a Spatial Analysis of Multiplexed Tissue Imaging Data</td> </tr> <tr class="row_odd"> <td><a href="html/TCGAWorkflow.html">TCGAWorkflow</a></td> <td>Tiago Chedraoui Silva </td> <td>TCGA Workflow Analyze cancer genomics and epigenomics data using Bioconductor packages</td> </tr> <tr class="row_even"> <td><a href="html/variants.html">variants</a></td> <td>Bioconductor Package Maintainer </td> <td>Annotating Genomic Variants</td> </tr> </table> </div> </section> </main> <footer> <div class="footer-container"> <div class="link-container"> <div class="link-container-inner"> <nav> <a href="/about/index.html"><h3>About</h3></a> <a href="/about/annual-reports/">Annual Reports</a> <a href="/about/collaborations/">Collaborations</a> <a href="/about/core-team/">Core Team</a> <a href="/about/mirrors/">Mirrors</a> <a href="/dashboard/">Dashboard</a> <a href="/about/">Project Details</a> <a href="/about/code-of-conduct/">Code of Conduct</a> </nav> <nav> <a href="/developers/index.html"><h3>Developers</h3></a> <a href="https://contributions.bioconductor.org/develop-overview.html">Package Guidelines</a> <a href="https://contributions.bioconductor.org/submission-overview.html">Package Submission</a> <a href="/developers/release-schedule/">Release Schedule</a> <a href="/about/release-announcements/">Release Announcements</a> <a href="https://contributions.bioconductor.org/git-version-control.html">Source Control</a> <a href="https://code.bioconductor.org/">Browsable Code Base</a> <a href="/checkResults/">Build Reports</a> </nav> </div> <div class="link-container-inner"> <nav> <a href="/help/index.html"><h3>Learn</h3></a> <a href="https://training.bioconductor.org/">Education and Training</a> <a href="/help/bioconductor-books/">Bioconductor Books</a> <a href="/help/package-vignettes/">Package Vignettes</a> <a href="/packages/release/workflows/">Workflows</a> <a href="/help/publications/">Publications</a> <a href="/help/community/">Community Resources</a> <a href="/help/support/">Get Help</a> </nav> <nav> <a href="/install/index.html"><h3>Get started</h3></a> <a href="/install/index.html#install-R">Install R</a> <a href="/install/index.html#find-bioconductor-packages">Find Bioconductor Packages</a> <a href="/install/index.html#install-bioconductor-packages">Install Bioconductor Packages</a> <a href="/install/index.html#update-bioconductor-packages">Update Bioconductor Packages</a> <a href="/help/docker/">Docker Images</a> <a href="https://anvil.bioconductor.org/">Bioconductor in AnVIL</a> <a href="/packages/release/BiocViews.html#___Software">Bioconductor Packages</a> </nav> </div> </div> <div class="logo-contact-container"> <div class="copyright"> <p> Contact us: <a class="text-underline" href="https://support.bioconductor.org/">support.bioconductor.org</a><br/> Copyright © 2003 - 2025 Bioconductor </p> </div> <div class="socials-logo-container"> <div class="socials"> <a href="https://slack.bioconductor.org/" target="_blank"><img alt="Slack Logo" src="/images/icons/slack.png" /></a> <a href="https://www.youtube.com/user/bioconductor" target="_blank"><img alt="YouTube Logo" src="/images/icons/svgs/youtube.svg" /></a> <a href="https://www.linkedin.com/company/bioconductor/" target="_blank"><img alt="LinkedIn Logo" src="/images/icons/svgs/linkedin.svg" /></a> <a href="https://bsky.app/profile/bioconductor.bsky.social" target="_blank"><img alt="Bluesky Logo" src="/images/icons/svgs/bluesky.svg" /></a> <a href="https://genomic.social/@bioconductor" target="_blank"><img alt="Mastodon Logo" src="/images/icons/svgs/mastodon.svg" /></a> <a href="https://blog.bioconductor.org/" target="_blank"><img alt="Blog Logo" src="/images/icons/svgs/arrow-circle-right-white.svg" /></a> </div> <img class="footer-logo" src="/images/logo/svg/BC-Logo-White.svg" alt="BioConductor Logo in White" /> </div> </div> </div> </footer> </body> </html>

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Bioconductor - 3.20 Workflow Packages