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Kevin Rue-Albrecht edited this page Sep 29, 2021 · 9 revisions

Lesson points

Brainstorm lesson points, and organise them thematically, to facilitate the design of episodes.

Introduction to Bioconductor

See the episode Introduction to Bioconductor.

  • Brief history of the Bioconductor project (e.g., timeline of milestones)
  • Core publications of the Bioconductor project (i.e., core infrastructure, not research papers simply using Bioconductor packages)
  • Relationship to the CRAN repository
  • Release cycle
  • Types of packages
  • The (main) Bioconductor website
  • Package classification using biocViews
  • Interoperability of Bioconductor packages
  • Education: Conferences, workshops, and courses
  • Communication: support website, Slack workspace, developers mailing list,
  • Governance: Scientific, Technical, and Community Advisory Boards (i.e., SAB, TAB, and CAB)
  • Code of Conduct (CoC) Committee

Installing Bioconductor

See the episode Installing Bioconductor.

  • Installing the BiocManager package
  • Bioconductor releases and their relationship to R versions
  • Versioning of Bioconductor packages
  • The release and devel branches of the Bioconductor repository
  • Installing Bioconductor packages
  • Checking for package updates
  • Updating Bioconductor packages
  • Finding packages using biocViews

Getting help

See the episode Getting help.

Using the local documentation installed with packages

  • Vignettes
  • Man pages

Using online documentation

  • Package landing pages
  • The Bioconductor website
  • Educational materials from courses and workshops
  • Workflow packages and vignettes

Asking for help

  • The Bioconductor support site
  • Issues on source code repositories (e.g., GitHub)
  • Why you should not email package developers directly

Working with biological strings

See the episode Biostrings.

  • Install the Biostrings package.
  • Motivation for representing biological strings as S4 objects
  • Representing a single DNA string
  • Importing a collection of DNA strings from a file
  • Examples of methods available to process biological strings

Bioconductor and Python

No episode yet.

  • The basilisk package
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