Day 2
Lecture 5 - Bioconductor 201
Developing R/Bioconductor packages for Genomics
Welcome
Program
Prerequesites
Extra resources
Day 1
Lecture 0 - Introduction to the workshop
Lecture 1 - R package architecture
Lecture 2 - Introduction to Bioconductor
Lecture 3 - R developer toolkit
Day 2
Lecture 4 - Continuous development
Lecture 5 - Bioconductor 201
Day 3
Lecture 6 - Git versioning
Lecture 8 - Vignettes and data
Day 4
Lecture 7 - S4 classes in Bioconductor
Lecture 9 - Bioconductor package submission
Day 5
Lecture 10 - Other package types
Lecture 11 - Package dissemination
Exercises
1
Getting started with Bioconductor ecosystem
2
Kickstarting an R package
3
Enriching package functionalities
4
Using S4 classes in a package
5
Improving package integration
Lecture 5 - Bioconductor 201
<div id="quarto-navigation-envelope" class="hidden"> <p><span class="hidden" data-render-id="quarto-int-sidebar-title">Developing R/Bioconductor packages for Genomics</span> <span class="hidden" data-render-id="quarto-int-navbar-title">Developing R/Bioconductor packages for Genomics</span> <span class="hidden" data-render-id="quarto-int-next">Lecture 6 - Git versioning</span> <span class="hidden" data-render-id="quarto-int-prev">Lecture 4 - Continuous development</span> <span class="hidden" data-render-id="quarto-int-sidebar:/index.html">Welcome</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/program.html">Program</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/prerequisites.html">Prerequesites</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/extra.html">Extra resources</span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-1">Day 1</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lecture0_course-overview.html">Lecture 0 - Introduction to the workshop</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lecture1_Package_architecture.html">Lecture 1 - R package architecture</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lecture2_Bioconductor_101.html">Lecture 2 - Introduction to Bioconductor</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lecture3_Developer-toolkit.html">Lecture 3 - R developer toolkit</span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-2">Day 2</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Lecture4_Continuous_development-writing-documenting-testing.html">Lecture 4 - Continuous development</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Lecture5_Bioconductor_201.html">Lecture 5 - Bioconductor 201</span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-3">Day 3</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Lecture6_Git_versionning.html">Lecture 6 - Git versioning</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Lecture7_Improving_package-data_vignettes-....html">Lecture 8 - Vignettes and data</span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-4">Day 4</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lecture8_S4_classes.html">Lecture 7 - S4 classes in Bioconductor</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lecture9_Bioconductor_submission.html">Lecture 9 - Bioconductor package submission</span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-5">Day 5</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day5/Lecture10_Other_package_types.html">Lecture 10 - Other package types</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day5/Lecture11_Package_dissemination.html">Lecture 11 - Package dissemination</span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-6">Exercises</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/exercises/Day1_Getting-started-with-Bioc.html"><span class="chapter-number">1</span> <span class="chapter-title">Getting started with Bioconductor ecosystem</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/exercises/Day2_Developer-virtuous-circle.html"><span class="chapter-number">2</span> <span class="chapter-title">Kickstarting an R package</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/exercises/Day3_Examples-test-data.html"><span class="chapter-number">3</span> <span class="chapter-title">Enriching package functionalities</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/exercises/Day4_S4-classes.html"><span class="chapter-number">4</span> <span class="chapter-title">Using S4 classes in a package</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/exercises/Day5_package-integration.html"><span class="chapter-number">5</span> <span class="chapter-title">Improving package integration</span></span> <span class="hidden" data-render-id="footer-left">Developing R/Bioconductor packages for Genomics |<br /> J. Serizay</span> <span class="hidden" data-render-id="footer-right">This book was built with <a href="https://quarto.org/">Quarto</a>.</span> <span class="hidden" data-render-id="quarto-breadcrumbs-5d0d9e50bf708684c2c6e57b56ae9e8c">Day 2</span> <span class="hidden" data-render-id="quarto-breadcrumbs-0b8c10d607b979bb536e1a61a1381895">Lecture 5 - Bioconductor 201</span></p> </div> <div id="quarto-meta-markdown" class="hidden"> <p><span class="hidden" data-render-id="quarto-metatitle">Developing R/Bioconductor packages for Genomics - Lecture 5 - Bioconductor 201</span> <span class="hidden" data-render-id="quarto-twittercardtitle">Developing R/Bioconductor packages for Genomics - Lecture 5 - Bioconductor 201</span> <span class="hidden" data-render-id="quarto-ogcardtitle">Developing R/Bioconductor packages for Genomics - Lecture 5 - Bioconductor 201</span> <span class="hidden" data-render-id="quarto-metasitename">Developing R/Bioconductor packages for Genomics</span> <span class="hidden" data-render-id="quarto-twittercarddesc"></span> <span class="hidden" data-render-id="quarto-ogcardddesc"></span></p> </div> </main> <!-- /main --> <script id = "quarto-html-after-body" type="application/javascript"> window.document.addEventListener("DOMContentLoaded", function (event) { const toggleBodyColorMode = (bsSheetEl) => { const mode = bsSheetEl.getAttribute("data-mode"); 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