{"id":13821484,"url":"https://github.com/griffithlab/rnaseq_tutorial","last_synced_at":"2025-05-15T17:04:29.757Z","repository":{"id":19245781,"uuid":"22481024","full_name":"griffithlab/rnaseq_tutorial","owner":"griffithlab","description":"Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.","archived":false,"fork":false,"pushed_at":"2023-05-31T18:45:10.000Z","size":459472,"stargazers_count":1363,"open_issues_count":6,"forks_count":618,"subscribers_count":181,"default_branch":"master","last_synced_at":"2025-04-07T22:07:50.243Z","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":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/griffithlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2014-07-31T18:58:09.000Z","updated_at":"2025-04-01T07:11:38.000Z","dependencies_parsed_at":"2022-08-07T09:01:13.776Z","dependency_job_id":"7ee22314-690b-4096-a5e0-029c3a8bbf5a","html_url":"https://github.com/griffithlab/rnaseq_tutorial","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Frnaseq_tutorial","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Frnaseq_tutorial/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Frnaseq_tutorial/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Frnaseq_tutorial/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/griffithlab","download_url":"https://codeload.github.com/griffithlab/rnaseq_tutorial/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254384987,"owners_count":22062422,"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":"2024-08-04T08:01:22.669Z","updated_at":"2025-05-15T17:04:24.748Z","avatar_url":"https://github.com/griffithlab.png","language":"R","funding_links":[],"categories":["R","Resources"],"sub_categories":["RNA-Seq"],"readme":"### Informatics for RNA-seq: A web resource for analysis on the cloud\n\nTHIS VERSION OF THE RNA-SEQ COURSE IS DEPRECATED. FOR CURRENT VERSION PLEASE VISIT: https://rnabio.org/\n\n\u003chr\u003e\n\nAn educational tutorial and working demonstration pipeline for RNA-seq analysis including an introduction to: cloud computing, next generation sequence file formats, reference genomes, gene annotation, expression analysis, differential expression analysis, alternative splicing analysis, data visualization, and interpretation.\n\nThis repository is used to store code and certain raw materials for a detailed RNA-seq tutorial.  To actually complete this tutorial, go to the \u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki\"\u003eRNA-seq tutorial wiki\u003c/a\u003e.\n\nCitation:\nMalachi Griffith\\*, Jason R. Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith\\*. 2015. \u003ca href=\"http://dx.doi.org/10.1371/journal.pcbi.1004393\"\u003eInformatics for RNA-seq: A web resource for analysis on the cloud\u003c/a\u003e. PLoS Comp Biol. 11(8):e1004393.\n\n\\*To whom correspondence should be addressed: E-mail: mgriffit[AT]genome.wustl.edu, ogriffit[AT]genome.wustl.edu\n\nNote: An archived version of this tutorial exists \u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1\"\u003ehere\u003c/a\u003e. This version is maintained for consistency with the published materials (\u003ca href=\"http://dx.doi.org/10.1371/journal.pcbi.1004393\"\u003eGriffith et al. 2015. PLoS Comp Biol.\u003c/a\u003e) and for past students wishing to review covered material. However, we strongly suggest that you continue with the current version of the tutorial below.\n\n### Want to contribute to the RNA-seq Wiki?\n\n[Fork it and send a pull request.](https://github.com/griffithlab/rnaseq_tutorial_wiki.git)\n\n\u003chr\u003e\n\n### Tutorial Table of Contents\n\u003col start=\"0\"\u003e\n  \u003cli\u003e\u003cstrong\u003eModule 0 - Introduction and Cloud Computing\u003c/strong\u003e\u003c/li\u003e\n  \u003col start=\"i\"\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Authors\"\u003eAuthors\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Citation\"\u003eCitation and Supplementary Materials\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Syntax\"\u003eSyntax\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Intro-to-AWS-Cloud-Computing\"\u003eIntro to AWS Cloud Computing\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Logging-into-Amazon-Cloud\"\u003eLogging into Amazon Cloud\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Unix-Bootcamp\"\u003eUnix Bootcamp\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Environment\"\u003eEnvironment\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Resources\"\u003eResources\u003c/a\u003e\u003c/li\u003e\n  \u003c/ol\u003e\n  \u003cli\u003e\u003cstrong\u003eModule 1 - Introduction to RNA sequencing\u003c/strong\u003e\u003c/li\u003e\n  \u003col start=\"i\"\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Installation\"\u003eInstallation\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Reference-Genome\"\u003eReference Genomes\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Annotation\"\u003eAnnotations\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Indexing\"\u003eIndexing\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/RNAseq-Data\"\u003eRNA-seq Data\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/PreAlignment-QC\"\u003ePre-Alignment QC\u003c/a\u003e\u003c/li\u003e\n  \u003c/ol\u003e\n  \u003cli\u003e\u003cstrong\u003eModule 2 - RNA-seq Alignment and Visualization\u003c/strong\u003e\u003c/li\u003e\n  \u003col start=\"i\"\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Adapter-Trim\"\u003eAdapter Trim\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Alignment\"\u003eAlignment\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/IGV-Tutorial\"\u003eIGV\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/PostAlignment-Visualization\"\u003eAlignment Visualization\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/PostAlignment-QC\"\u003eAlignment QC\u003c/a\u003e\u003c/li\u003e\n  \u003c/ol\u003e\n  \u003cli\u003e\u003cstrong\u003eModule 3 - Expression and Differential Expression\u003c/strong\u003e\u003c/li\u003e\n  \u003col start=\"i\"\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Expression\"\u003eExpression\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Differential-Expression\"\u003eDifferential Expression\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/DE-Visualization\"\u003eDE Visualization\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Kallisto\"\u003eKallisto for Reference-Free Abundance Estimation\u003c/a\u003e\u003c/li\u003e\n  \u003c/ol\u003e\n  \u003cli\u003e\u003cstrong\u003eModule 4 - Isoform Discovery and Alternative Expression\u003c/strong\u003e\u003c/li\u003e\n  \u003col start=\"i\"\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Reference-Guided-Transcript-Assembly\"\u003eReference Guided Transcript Assembly\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/de-novo-Transcript-Assembly\"\u003ede novo Transcript Assembly\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Transcript-Assembly-Merge\"\u003eTranscript Assembly Merge\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Differential-Splicing\"\u003eDifferential Splicing\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Transcript-Assembly-Visualization\"\u003eSplicing Visualization\u003c/a\u003e\u003c/li\u003e\n  \u003c/ol\u003e\n  \u003cli\u003e\u003cstrong\u003eModule 5 - De novo transcript reconstruction\u003c/strong\u003e\u003c/li\u003e\n    \u003col start=\"i\"\u003e\n    \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Trinity-Assembly-And-Analysis\"\u003eDe novo RNA-Seq Assembly and Analysis Using Trinity\u003c/a\u003e\u003c/li\u003e\n    \u003c/ol\u003e\n  \u003cli\u003e\u003cstrong\u003eModule 6 - Functional Annotation of Transcripts\u003c/strong\u003e\u003c/li\u003e\n    \u003col start=\"i\"\u003e\n    \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Trinotate-Functional-Annotation\"\u003eFunctional Annotation of Assembled Transcripts Using Trinotate\u003c/a\u003e\u003c/li\u003e\n    \u003c/ol\u003e\n  \u003cli\u003e\u003cstrong\u003eAppendix\u003c/strong\u003e\u003c/li\u003e\n  \u003col start=\"i\"\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Saving-Your-Results\"\u003eSaving Your Results\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Abbreviations\"\u003eAbbreviations\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Lectures\"\u003eLectures\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Solutions\"\u003ePractical Exercise Solutions\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Integrated-Assignment\"\u003eIntegrated Assignment\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/Proposed-Improvements\"\u003eProposed Improvements\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial/wiki/AWS-Setup\"\u003eAWS Setup\u003c/a\u003e\u003c/li\u003e\n  \u003c/ol\u003e\n\u003c/ol\u003e\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Frnaseq_tutorial","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgriffithlab%2Frnaseq_tutorial","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Frnaseq_tutorial/lists"}