{"id":19623933,"url":"https://github.com/bioconductor/learnbioconductor","last_synced_at":"2025-08-20T00:04:52.121Z","repository":{"id":20551881,"uuid":"23831702","full_name":"Bioconductor/LearnBioconductor","owner":"Bioconductor","description":"Training material for introductory R / Bioconductor courses","archived":false,"fork":false,"pushed_at":"2023-03-15T20:25:16.000Z","size":3541,"stargazers_count":78,"open_issues_count":0,"forks_count":35,"subscribers_count":28,"default_branch":"devel","last_synced_at":"2025-04-28T05:34:54.245Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","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}},"created_at":"2014-09-09T12:03:39.000Z","updated_at":"2025-04-06T21:43:33.000Z","dependencies_parsed_at":"2023-10-20T18:25:45.718Z","dependency_job_id":null,"html_url":"https://github.com/Bioconductor/LearnBioconductor","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Bioconductor/LearnBioconductor","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FLearnBioconductor","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FLearnBioconductor/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FLearnBioconductor/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FLearnBioconductor/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Bioconductor","download_url":"https://codeload.github.com/Bioconductor/LearnBioconductor/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FLearnBioconductor/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":271242036,"owners_count":24724978,"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","status":"online","status_checked_at":"2025-08-19T02:00:09.176Z","response_time":63,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2024-11-11T11:36:08.798Z","updated_at":"2025-08-20T00:04:52.053Z","avatar_url":"https://github.com/Bioconductor.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"Learning R / Bioconductor for Sequence Analysis\n===============================================\n\nFred Hutchinson Cancer Research Center, Seattle, WA\u003cbr /\u003e\nOctober 27-29\n\nLocation: October 27 / 28: Arnold Building M1-A303; October 29:\nThomas D1-080\n\nContact: Martin Morgan (content,\n[mtmorgan@fhcrc.org](mailto:mtmorgan@fhcrc.org)); Melissa Alvendia\n(administration, [malvendia@fhcrc.org](mailto:malvendia@fhcrc.org))\n\nThis course is directed at beginning and intermediate users who would\nlike an introduction to the analysis and comprehension of\nhigh-throughput sequence data using _R_ and\n_[Bioconductor](http://bioconductor.org)_. Day 1 focuses on learning\nessential background: an introduction to the _R_ programming language;\ncentral concepts for effective use of _Bioconductor_ software; and an\noverview of high-throughput sequence analysis work flows. Day 2\nemphasizes use of _Bioconductor_ for specific tasks: an RNA-seq\ndifferential expression work flow; exploratory, machine learning, and\nother statistical tasks; gene set enrichment; and annotation.  Day 3\ntransitions to understanding effective approaches for managing larger\nchallenges: strategies for working with large data, writing re-usable\nfunctions, developing reproducible reports and work flows, and\nvisualizing results.  The course combines lectures with extensive\nhands-on practicals; students are required to bring a laptop with\nwireless internet access and a modern version of the Chrome or Safari\nweb browser.\n\nSchedule (tentative)\n--------------------\n\nDay 1: Learn _R_ / _Bioconductor_\n\n- 9:00 - 10:30 Introduction to _R_: objects, functions, help!\n- 11:00 - 12:30 Introduction to _Bioconductor_: working with packages and classes\n- 1:30 - 5:00 (break: 3:00 - 3:30) Introduction to sequence analysis:\n  typical work flow; data types and quality assessment; essential\n  _Bioconductor_ packages\n\nDay 2: Use _R_ / _Bioconductor_ \n\n- 9:00 - 12:30 (break (10:30 - 11:00) An RNA-seq differential\n  expression work flow (detail)\n- 1:30 - 2:00 Other work flows (survey): ChIP-seq, variants, copy\n  number, epigenomics\n- 2:00 - 3:00 Machine learning; exploratory and other statistical\n  analysis\n- 3:30 - 4:00 Annotating genes, genomes, and variants\n- 4:00 - 5:00 Approaches to gene set enrichment\n\nDay 3: Develop Skills and Best Practices\n\n- 9:00 - 10:30 Working with large data\n- 11:00 - 12:30 Organizing code in functions, files, and packages\n- 1:30 - 3:00 Reproducible reports and work flows: markdown\n- 3:30 - 4:30 Visualization\n- 4:30 - 5:00 Summary\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Flearnbioconductor","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioconductor%2Flearnbioconductor","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Flearnbioconductor/lists"}