{"id":13544267,"url":"https://github.com/Bioconductor/UseBioconductor","last_synced_at":"2025-04-02T14:30:43.100Z","repository":{"id":26535282,"uuid":"29988538","full_name":"Bioconductor/UseBioconductor","owner":"Bioconductor","description":"Training material for intermediate R / Bioconductor courses","archived":false,"fork":false,"pushed_at":"2023-03-15T20:25:40.000Z","size":4485,"stargazers_count":17,"open_issues_count":0,"forks_count":6,"subscribers_count":19,"default_branch":"devel","last_synced_at":"2025-03-19T15:14:44.621Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"toineheuvelmans/Metron","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}},"created_at":"2015-01-28T21:13:32.000Z","updated_at":"2024-06-07T03:53:43.000Z","dependencies_parsed_at":"2024-01-14T02:39:06.254Z","dependency_job_id":"30eff784-3323-4820-8fdc-e5607020f616","html_url":"https://github.com/Bioconductor/UseBioconductor","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FUseBioconductor","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FUseBioconductor/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FUseBioconductor/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FUseBioconductor/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Bioconductor","download_url":"https://codeload.github.com/Bioconductor/UseBioconductor/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246832104,"owners_count":20841112,"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":[],"created_at":"2024-08-01T11:00:44.748Z","updated_at":"2025-04-02T14:30:39.715Z","avatar_url":"https://github.com/Bioconductor.png","language":"R","funding_links":[],"categories":["Educational resources"],"sub_categories":["Bioconductor"],"readme":"Use R / Bioconductor for Sequence Analysis\n==========================================\n\nFred Hutchinson Cancer Research Center, Seattle, WA\u003cbr /\u003e\n6-7 April, 2015\n\nContact: Martin Morgan\n([mtmorgan@fredhutch.org](mailto:mtmorgan@fredhutch.org))\n\nThis **INTERMEDIATE** course is designed for individuals comfortable\nusing _R_, and with some familiarity with _Bioconductor_. It consists\nof approximately equal parts lecture and practical sessions addressing\nuse of _Bioconductor_ software for analysis and comprehension of\nhigh-throughput sequence and related data. Specific topics include use\nof central Bioconductor classes (e.g., _GRanges_,\n_SummarizedExperiment_), RNASeq gene differential expression, ChIP-seq\nand methylation work flows, approaches to management and integrative\nanalysis of diverse high-throughput data types, and strategies for\nworking with large data. Participants are required to bring a laptop\nwith wireless internet access and a modern version of the Chrome or\nSafari web browser.\n\nRegistration\n------------\n\nPlease register [online](https://register.bioconductor.org/Seattle-Apr-2015/).\n\nSchedule (tentative)\n--------------------\n\nDay 1 (9:00 - 12:30; 1:30 - 5:00)\n\n- [A. Introduction](vignettes/A_Introduction.Rmd). _Bioconductor_ and\n  sequencing work flows\n- [B. Genomic Ranges](vignettes/B_GenomicRanges.Rmd). Working with Genomic\n  Ranges and other _Bioconductor_ data structures (e.g., in the\n  [GenomicRanges](http://bioconductor.org/packages/devel/bioc/html/GenomicRanges.html).\n  package).  \n- [C. Differential Gene Expression](vignettes/C_DifferentialExpression.Rmd). RNA-Seq\n  known gene differential expression with\n  [DESeq2](http://bioconductor.org/packages/devel/bioc/html/DESeq2.html)\n  and\n  [edgeR](http://bioconductor.org/packages/devel/bioc/html/edgeR.html).\n\nDay 2 (9:00 - 12:30; 1:30 - 5:00)\n\n- [D. Machine Learning](vignettes/D_MachineLearning.Rmd).\n- [E. Gene Set Enrichment](vignettes/E_GeneSetEnrichment.Rmd).\n- [F. ChIP-seq](vignettes/F_ChIPSeq.Rmd) ChIP-seq with\n  [csaw](http://bioconductor.org/packages/devel/bioc/html/csaw.html)\n- [I. Large Data](vignettes/I_LargeData.Rmd) -- efficient, parallel, and cloud\n  programming with\n  [BiocParallel](http://bioconductor.org/packages/devel/bioc/html/BiocParallel.html),\n  [GenomicFiles](http://bioconductor.org/packages/devel/bioc/html/GenomicFiles.html),\n  and other resources.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FBioconductor%2FUseBioconductor","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FBioconductor%2FUseBioconductor","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FBioconductor%2FUseBioconductor/lists"}