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https://github.com/bioconductor/bioconductor-training

Bioconductor teaching and education committee
https://github.com/bioconductor/bioconductor-training

bioconductor committee education teaching training

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Bioconductor teaching and education committee

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README 

        
# 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](http://bioconductor.org/about/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](https://carpentries-incubator.github.io/bioc-intro/)

  The **Data science** lesson is based on the [Carpentries Ecology

  Curriculum](https://datacarpentry.org/lessons/#ecology-workshop). 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](https://carpentries-incubator.github.io/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](https://carpentries-incubator.github.io/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](https://carpentries-incubator.github.io/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](https://docs.google.com/document/d/1s2QMk5XA-uhBVprAO3ZDk1Yfv1cnUWLp9zdvYq9Feu4/edit#).



## Discussions



- The `education-and-training` channel on the [Bioconductor community

  slack](https://slack.bioconductor.org/).

- The [Google group](https://groups.google.com/g/bioconductor-teaching/) (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](https://www.bioconductor.org/help/events/). 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.