{"id":19624046,"url":"https://github.com/bioconductor/bioconductor-training","last_synced_at":"2026-01-27T01:33:03.930Z","repository":{"id":41812242,"uuid":"288169645","full_name":"Bioconductor/bioconductor-training","owner":"Bioconductor","description":"Bioconductor teaching and education committee","archived":false,"fork":false,"pushed_at":"2025-02-26T10:38:57.000Z","size":71988,"stargazers_count":48,"open_issues_count":8,"forks_count":26,"subscribers_count":21,"default_branch":"devel","last_synced_at":"2025-02-26T11:33:53.480Z","etag":null,"topics":["bioconductor","committee","education","teaching","training"],"latest_commit_sha":null,"homepage":"https://training.bioconductor.org/","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Bioconductor.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-08-17T12:05:43.000Z","updated_at":"2025-02-26T10:32:20.000Z","dependencies_parsed_at":"2025-02-10T16:38:38.663Z","dependency_job_id":null,"html_url":"https://github.com/Bioconductor/bioconductor-training","commit_stats":null,"previous_names":["bioconductor/bioconductor-training","bioconductor/bioconductor-teaching"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbioconductor-training","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbioconductor-training/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbioconductor-training/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbioconductor-training/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Bioconductor","download_url":"https://codeload.github.com/Bioconductor/bioconductor-training/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240922476,"owners_count":19879113,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioconductor","committee","education","teaching","training"],"created_at":"2024-11-11T11:36:41.183Z","updated_at":"2026-01-27T01:33:03.922Z","avatar_url":"https://github.com/Bioconductor.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# The Bioconductor training committee\n\nThe Bioconductor training committee is a collaborative effort to\nconsolidate Bioconductor-focused training material and establish\na community of Bioconductor trainers. We define a curriculum and\nimplement online lessons for beginner and more advanced R users\nwho want to learn to analyse their data with Bioconductor packages.\n\nThe Bioconductor training committee reports to the Bioconductor\n[Community Advisory Board](http://bioconductor.org/about/community-advisory-board/).\nIt is currently chaired by Charlotte Soneson and Laurent Gatto.\nThere’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.\n\nThis meta-repository is used for general discussions. The respective\nlessons are developed as modules in their own repositories.\n\n## Publications\n\n**Learning and teaching biological data science in the Bioconductor community**  \nDrnevich, Tan et al. (2025)  \nPublished in *PLOS Computational Biology*\n\n👉 [Read the full paper](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012925)\n\n## Modules\n\n- [bioc-intro](https://carpentries-incubator.github.io/bioc-intro/)\n  The **Data science** lesson is based on the [Carpentries Ecology\n  Curriculum](https://datacarpentry.org/lessons/#ecology-workshop). There\n  are no pre-requisites for this module, and the materials assume no\n  prior knowledge about R and Bioconductor. It introduces R, RStudio,\n  teaches data cleaning, management, analysis, and visualisation and\n  introduces some Bioconductor concepts. Notes are collated in\n  `bioc-intro.md` in this repo.\n\n- [bioc-rnaseq](https://carpentries-incubator.github.io/bioc-rnaseq/)\n **Analysis and interpretation of bulk RNA sequencing data with\n  Bioconductor** shows how to use Bioconductor packages to analyse\n  bulk RNA-seq data. It expects good familiarity with R and the\n  Bioconductor project.\n\n- [bioc-scrnaseq](https://carpentries-incubator.github.io/bioc-scrnaseq/)\n  **Analysis and interpretation of single-cell RNA sequencing data with\n  Bioconductor** shows how to use Bioconductor packages for essential single-cell\n  analysis steps including quality control, cell type annotation, multi-sample\n  analysis, working with large data, and integration with public data.\n  Pre-requisites include familiarity with R and Bioconductor. Familiarity with\n  bulk RNA-seq data analysis is beneficial, but not strictly required.    \n\n- [bioc-project](https://carpentries-incubator.github.io/bioc-project/)\n  The **Bioconductor project** lesson provides an introduction to the\n  Bioconductor project such as the Bioconductor home page, packages,\n  package landing pages, and package vignettes, where to find help,\n  Bioconductor workflows, Bioconductor release schedule and versions,\n  some core infrastructure, ... It is meant to be use in combination\n  with other modules as part of a wider workshop.\n\n### New lessons\n\nIf you are interested in contributing new lessons or Carpentry modules,\nfeel free to get in touch with the teaching committee via Zulip or the\ngoogle group (see below). We would be happy to discuss and/or contribute\nto anything related to the lesson design, general help with the long-term\nmaintenance, dissemination of the lesson, or any help/topic you can think of.\n\n## Material design and maintenance\n\n### Lesson design\n\n- Use RStudio for teaching.\n- If possible, finish lessons with a *Next steps* section to highlight\n  other relevant Bioconductor lessons. Similarly, in the Summary and\n  Setup section, refer to other Bioconductor lessons that cover the\n  pre-requisites.\n- Whenever relevant, use Bioconductor recommended/maintained classes.\n- Package installation: favour `BiocManager::install()` for all\n  packages.\n- The bioc-intro lesson, which is based on the Ecology lesson, focuses\n  on the tidyverse.\n\n### Maintenance\n\n**Maintenance team** Each Bioconductor lesson has at least one\nmaintainer, and more generally a team of instructors that built and\nadviser on the maintenance of the lesson collaboratively. The\nmaintainer is the person that takes responsibility for merging the PRs\nand fixing build issues if/when they happen. The Carpentries\nCurriculum Advisory Committee Consultation Rubric provides a template\nas to how to address changes to the lessons.\n\n**Contributing and handling minor changes** For minor changes such as\ntypos or simple rephrasing can be submitted directly through a Github\npull request. The lesson maintainer can assess the PR, ask for\nclarifications or amendments and eventually merge the pull request.\n\n**Contributing and handling big changes** For more substantial changes,\nwe advise to first open an issue to discuss these changes with the\nmaintainer, the team that created the lesson, and other instructors\nthat have experience teaching the episode. A pull request for such a\nmore substantial change (and here, we deliberately don’t define them\nexplicitly and leave it to the lesson maintainer to assess the\nimportance), would be discussed in (1) the Github pull request and/or\n(2) on the bioconductor-teaching google group and/or, if necessary (3)\nduring a Bioconductor teaching monthly meeting. For the latter, it\nwould be recommended that at least 2 to 3 people that were part in the\ndesign of the lesson and/or that have teaching experience would be\npresent in addition to the lesson maintainer. The PR submitter is also\nwelcome to join the discussion.\n\n\n## Notes and meetings\n\n- [Governance document](resources/bioc-training-governance-v1.0.0.pdf)\n- Collaborative [Google\n  doc](https://docs.google.com/document/d/1s2QMk5XA-uhBVprAO3ZDk1Yfv1cnUWLp9zdvYq9Feu4/edit#).\n\n## Discussions\n\n- The `education-and-training` channel on the [Bioconductor community\n  chat](https://chat.bioconductor.org/).\n- The [Google group](https://groups.google.com/g/bioconductor-teaching/) (low-traffic, mainly used to send a reminder for the monthly meeting).  \n\n## Events\n\nExplore 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.  \n\n## Contact\n\nIf you are interested in this project and want to get in touch or\nparticipate, please contact the group via the Google group or\nindividual members on [Bioconductor Chat](https://chat.bioconductor.org) or by email.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fbioconductor-training","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioconductor%2Fbioconductor-training","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fbioconductor-training/lists"}