Day 1
Lecture 1 - R package architecture
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
Day 1
Lecture 1 - R package architecture
Lecture 1 - R package architecture
<div id="quarto-navigation-envelope" class="hidden"> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyLXRpdGxl">Developing R/Bioconductor packages for Genomics</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1uYXZiYXItdGl0bGU=">Developing R/Bioconductor packages for Genomics</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1uZXh0">Lecture 2 - Introduction to Bioconductor</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1wcmV2">Lecture 0 - Introduction to the workshop</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9pbmRleC5odG1sV2VsY29tZQ==">Welcome</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L3Byb2dyYW0uaHRtbFByb2dyYW0=">Program</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L3ByZXJlcXVpc2l0ZXMuaHRtbFByZXJlcXVlc2l0ZXM=">Prerequesites</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2V4dHJhLmh0bWxFeHRyYS1yZXNvdXJjZXM=">Extra resources</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOnF1YXJ0by1zaWRlYmFyLXNlY3Rpb24tMQ==">Day 1</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2RheTEvTGVjdHVyZTBfY291cnNlLW92ZXJ2aWV3Lmh0bWxMZWN0dXJlLTAtLS1JbnRyb2R1Y3Rpb24tdG8tdGhlLXdvcmtzaG9w">Lecture 0 - Introduction to the workshop</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2RheTEvTGVjdHVyZTFfUGFja2FnZV9hcmNoaXRlY3R1cmUuaHRtbExlY3R1cmUtMS0tLVItcGFja2FnZS1hcmNoaXRlY3R1cmU=">Lecture 1 - R package architecture</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2RheTEvTGVjdHVyZTJfQmlvY29uZHVjdG9yXzEwMS5odG1sTGVjdHVyZS0yLS0tSW50cm9kdWN0aW9uLXRvLUJpb2NvbmR1Y3Rvcg==">Lecture 2 - Introduction to Bioconductor</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2RheTEvTGVjdHVyZTNfRGV2ZWxvcGVyLXRvb2xraXQuaHRtbExlY3R1cmUtMy0tLVItZGV2ZWxvcGVyLXRvb2xraXQ=">Lecture 3 - R developer toolkit</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOnF1YXJ0by1zaWRlYmFyLXNlY3Rpb24tMg==">Day 2</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2RheTIvTGVjdHVyZTRfQ29udGludW91c19kZXZlbG9wbWVudC13cml0aW5nLWRvY3VtZW50aW5nLXRlc3RpbmcuaHRtbExlY3R1cmUtNC0tLUNvbnRpbnVvdXMtZGV2ZWxvcG1lbnQ=">Lecture 4 - Continuous development</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2RheTIvTGVjdHVyZTVfQmlvY29uZHVjdG9yXzIwMS5odG1sTGVjdHVyZS01LS0tQmlvY29uZHVjdG9yLTIwMQ==">Lecture 5 - Bioconductor 201</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOnF1YXJ0by1zaWRlYmFyLXNlY3Rpb24tMw==">Day 3</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2RheTMvTGVjdHVyZTZfR2l0X3ZlcnNpb25uaW5nLmh0bWxMZWN0dXJlLTYtLS1HaXQtdmVyc2lvbmluZw==">Lecture 6 - Git versioning</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2RheTMvTGVjdHVyZTdfSW1wcm92aW5nX3BhY2thZ2UtZGF0YV92aWduZXR0ZXMtLi4uLmh0bWxMZWN0dXJlLTgtLS1WaWduZXR0ZXMtYW5kLWRhdGE=">Lecture 8 - Vignettes and data</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOnF1YXJ0by1zaWRlYmFyLXNlY3Rpb24tNA==">Day 4</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2RheTQvTGVjdHVyZThfUzRfY2xhc3Nlcy5odG1sTGVjdHVyZS03LS0tUzQtY2xhc3Nlcy1pbi1CaW9jb25kdWN0b3I=">Lecture 7 - S4 classes in Bioconductor</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2RheTQvTGVjdHVyZTlfQmlvY29uZHVjdG9yX3N1Ym1pc3Npb24uaHRtbExlY3R1cmUtOS0tLUJpb2NvbmR1Y3Rvci1wYWNrYWdlLXN1Ym1pc3Npb24=">Lecture 9 - Bioconductor package submission</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOnF1YXJ0by1zaWRlYmFyLXNlY3Rpb24tNQ==">Day 5</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2RheTUvTGVjdHVyZTEwX090aGVyX3BhY2thZ2VfdHlwZXMuaHRtbExlY3R1cmUtMTAtLS1PdGhlci1wYWNrYWdlLXR5cGVz">Lecture 10 - Other package types</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2RheTUvTGVjdHVyZTExX1BhY2thZ2VfZGlzc2VtaW5hdGlvbi5odG1sTGVjdHVyZS0xMS0tLVBhY2thZ2UtZGlzc2VtaW5hdGlvbg==">Lecture 11 - Package dissemination</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOnF1YXJ0by1zaWRlYmFyLXNlY3Rpb24tNg==">Exercises</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2V4ZXJjaXNlcy9EYXkxX0dldHRpbmctc3RhcnRlZC13aXRoLUJpb2MuaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+MTwvc3Bhbj4tLTxzcGFuLWNsYXNzPSdjaGFwdGVyLXRpdGxlJz5HZXR0aW5nLXN0YXJ0ZWQtd2l0aC1CaW9jb25kdWN0b3ItZWNvc3lzdGVtPC9zcGFuPg=="><span class="chapter-number">1</span> <span class="chapter-title">Getting started with Bioconductor ecosystem</span></span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2V4ZXJjaXNlcy9EYXkyX0RldmVsb3Blci12aXJ0dW91cy1jaXJjbGUuaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+Mjwvc3Bhbj4tLTxzcGFuLWNsYXNzPSdjaGFwdGVyLXRpdGxlJz5LaWNrc3RhcnRpbmctYW4tUi1wYWNrYWdlPC9zcGFuPg=="><span class="chapter-number">2</span> <span class="chapter-title">Kickstarting an R package</span></span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2V4ZXJjaXNlcy9EYXkzX0V4YW1wbGVzLXRlc3QtZGF0YS5odG1sPHNwYW4tY2xhc3M9J2NoYXB0ZXItbnVtYmVyJz4zPC9zcGFuPi0tPHNwYW4tY2xhc3M9J2NoYXB0ZXItdGl0bGUnPkVucmljaGluZy1wYWNrYWdlLWZ1bmN0aW9uYWxpdGllczwvc3Bhbj4="><span class="chapter-number">3</span> <span class="chapter-title">Enriching package functionalities</span></span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2V4ZXJjaXNlcy9EYXk0X1M0LWNsYXNzZXMuaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+NDwvc3Bhbj4tLTxzcGFuLWNsYXNzPSdjaGFwdGVyLXRpdGxlJz5Vc2luZy1TNC1jbGFzc2VzLWluLWEtcGFja2FnZTwvc3Bhbj4="><span class="chapter-number">4</span> <span class="chapter-title">Using S4 classes in a package</span></span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWludC1zaWRlYmFyOi9jb250ZW50L2V4ZXJjaXNlcy9EYXk1X3BhY2thZ2UtaW50ZWdyYXRpb24uaHRtbDxzcGFuLWNsYXNzPSdjaGFwdGVyLW51bWJlcic+NTwvc3Bhbj4tLTxzcGFuLWNsYXNzPSdjaGFwdGVyLXRpdGxlJz5JbXByb3ZpbmctcGFja2FnZS1pbnRlZ3JhdGlvbjwvc3Bhbj4="><span class="chapter-number">5</span> <span class="chapter-title">Improving package integration</span></span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWJyZWFkY3J1bWJzLURheS0x">Day 1</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLWJyZWFkY3J1bWJzLUxlY3R1cmUtMS0tLVItcGFja2FnZS1hcmNoaXRlY3R1cmU=">Lecture 1 - R package architecture</span></p> <div class="hidden quarto-markdown-envelope-contents" data-render-id="Zm9vdGVyLWxlZnQ="> <p>Developing R/Bioconductor packages for Genomics |<br> J. Serizay</p> </div> <div class="hidden quarto-markdown-envelope-contents" data-render-id="Zm9vdGVyLXJpZ2h0"> <p>This book was built with <a href="https://quarto.org/">Quarto</a>.</p> </div> </div> <div id="quarto-meta-markdown" class="hidden"> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLW1ldGF0aXRsZQ==">Lecture 1 - R package architecture – Developing R/Bioconductor packages for Genomics</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLXR3aXR0ZXJjYXJkdGl0bGU=">Lecture 1 - R package architecture – Developing R/Bioconductor packages for Genomics</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLW9nY2FyZHRpdGxl">Lecture 1 - R package architecture – Developing R/Bioconductor packages for Genomics</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLW1ldGFzaXRlbmFtZQ==">Developing R/Bioconductor packages for Genomics</span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLXR3aXR0ZXJjYXJkZGVzYw=="></span></p> <p><span class="hidden quarto-markdown-envelope-contents" data-render-id="cXVhcnRvLW9nY2FyZGRkZXNj"></span></p> </div>
Lecture 0 - Introduction to the workshop
Lecture 2 - Introduction to Bioconductor