The Bioconductor training committee

The Bioconductor training committee is a collaborative effort to consolidate Bioconductor-focused training material and establish a community of Bioconductor trainers. We define a curriculum and implement online lessons for beginner and more advanced R users who want to learn to analyse their data with Bioconductor packages.

The Bioconductor training committee reports to the Bioconductor Community Advisory Board. It is currently chaired by Charlotte Soneson and Laurent Gatto. There’s no formal joining process or minimum commitment required — simply attend one of the monthly meetings (announced on the Google group, see below) or engage in our discussions to become a part of our community.

This meta-repository is used for general discussions. The respective lessons are developed as modules in their own repositories.

Modules

• bioc-intro The Data science lesson is based on the Carpentries Ecology Curriculum. There are no pre-requisites for this module, and the materials assume no prior knowledge about R and Bioconductor. It introduces R, RStudio, teaches data cleaning, management, analysis, and visualisation and introduces some Bioconductor concepts. Notes are collated in bioc-intro.md in this repo.

• bioc-rnaseq Analysis and interpretation of bulk RNA sequencing data with Bioconductor shows how to use Bioconductor packages to analyse bulk RNA-seq data. It expects good familiarity with R and the Bioconductor project.

• bioc-scrnaseq Analysis and interpretation of single-cell RNA sequencing data with Bioconductor shows how to use Bioconductor packages for essential single-cell analysis steps including quality control, cell type annotation, multi-sample analysis, working with large data, and integration with public data. Pre-requisites include familiarity with R and Bioconductor. Familiarity with bulk RNA-seq data analysis is beneficial, but not strictly required.

• bioc-project The Bioconductor project lesson provides an introduction to the Bioconductor project such as the Bioconductor home page, packages, package landing pages, and package vignettes, where to find help, Bioconductor workflows, Bioconductor release schedule and versions, some core infrastructure, ... It is meant to be use in combination with other modules as part of a wider workshop.

New lessons

If you are interested in contributing new lessons or Carpentry modules, feel free to get in touch with the teaching committee via slack of the google group (see below). We would be happy to discuss and/or contribute to anything related to the lesson design, general help with the long-term maintenance, dissemination of the lesson, or any help/topic you can think of.

Material design and maintenance

Lesson design

• Use RStudio for teaching.
• If possible, finish lessons with a Next steps section to highlight other relevant Bioconductor lessons. Similarly, in the Summary and Setup section, refer to other Bioconductor lessons that cover the pre-requisites.
• Whenever relevant, use Bioconductor recommended/maintained classes.
• Package installation: favour BiocManager::install() for all packages.
• The bioc-intro lesson, which is based on the Ecology lesson, focuses on the tidyverse.

Maintenance

Maintenance team Each Bioconductor lesson has at least one maintainer, and more generally a team of instructors that built and adviser on the maintenance of the lesson collaboratively. The maintainer is the person that takes responsibility for merging the PRs and fixing build issues if/when they happen. The Carpentries Curriculum Advisory Committee Consultation Rubric provides a template as to how to address changes to the lessons.

Contributing and handling minor changes For minor changes such as typos or simple rephrasing can be submitted directly through a Github pull request. The lesson maintainer can assess the PR, ask for clarifications or amendments and eventually merge the pull request.

Contributing and handling big changes For more substantial changes, we advise to first open an issue to discuss these changes with the maintainer, the team that created the lesson, and other instructors that have experience teaching the episode. A pull request for such a more substantial change (and here, we deliberately don’t define them explicitly and leave it to the lesson maintainer to assess the importance), would be discussed in (1) the Github pull request and/or (2) on the bioconductor-teaching google group and/or, if necessary (3) during a Bioconductor teaching monthly meeting. For the latter, it would be recommended that at least 2 to 3 people that were part in the design of the lesson and/or that have teaching experience would be present in addition to the lesson maintainer. The PR submitter is also welcome to join the discussion.

Notes and meetings

• Collaborative Google doc.

Discussions

• The education-and-training channel on the Bioconductor community slack.
• The Google group (low-traffic, mainly used to send a reminder for the monthly meeting).

Events

Explore upcoming opportunities and past Bioconductor workshops and training sessions on our events page. Interested in sharing your own Bioconductor training event with the community? Learn how to add your event directly through this page.

Contact

If you are interested in this project and want to get in touch or participate, please contact the group via the Google group or individual members on slack or by email.