{"id":19857113,"url":"https://github.com/griffithlab/rnaseq_tutorial_v1","last_synced_at":"2025-05-02T02:30:34.054Z","repository":{"id":78129943,"uuid":"73637119","full_name":"griffithlab/rnaseq_tutorial_v1","owner":"griffithlab","description":"Archive of original RNAseq.wiki tutorial that accompanied PLoS Comp Bio paper","archived":false,"fork":false,"pushed_at":"2016-11-13T20:52:46.000Z","size":96746,"stargazers_count":13,"open_issues_count":0,"forks_count":7,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-06T21:05:26.758Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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":"2016-11-13T19:17:12.000Z","updated_at":"2024-10-17T20:07:50.000Z","dependencies_parsed_at":"2023-02-26T02:00:29.581Z","dependency_job_id":null,"html_url":"https://github.com/griffithlab/rnaseq_tutorial_v1","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/griffithlab%2Frnaseq_tutorial_v1","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Frnaseq_tutorial_v1/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Frnaseq_tutorial_v1/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Frnaseq_tutorial_v1/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/griffithlab","download_url":"https://codeload.github.com/griffithlab/rnaseq_tutorial_v1/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251972410,"owners_count":21673599,"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":"2024-11-12T14:17:30.766Z","updated_at":"2025-05-02T02:30:29.042Z","avatar_url":"https://github.com/griffithlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"##NOTE: You are on the archive version of this RNA-seq analysis tutorial. 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 visit the current version of this tutorial at www.rnaseq.wiki. \n\n###Informatics for RNA-seq: A web resource for analysis on the cloud\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_v1/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\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_v1/wiki/Authors\"\u003eAuthors\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Citation\"\u003eCitation and Supplementary Materials\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Syntax\"\u003eSyntax\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/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_v1/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_v1/wiki/Unix-Bootcamp\"\u003eUnix Bootcamp\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Environment\"\u003eEnvironment\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/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_v1/wiki/Installation\"\u003eInstallation\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Reference-Genome\"\u003eReference Genome\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Annotation\"\u003eAnnotation\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Indexing\"\u003eIndexing\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/RNAseq-Data\"\u003eRNA-seq Data\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/PreAlignment-QC\"\u003ePreAlignment 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_v1/wiki/Adapter-Trim\"\u003eAdapter Trim\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Alignment\"\u003eAlignment\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/IGV-Tutorial\"\u003eIGV\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/PostAlignment-Visualization\"\u003ePostAlignment Visualization\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/PostAlignment-QC\"\u003ePostAlignment 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_v1/wiki/Expression\"\u003eExpression\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Differential-Expression\"\u003eDifferential Expression\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/DE-Visualization\"\u003eDE Visualization\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_v1/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_v1/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_v1/wiki/Transcript-Assembly-Merge\"\u003eTranscript Assembly Merge\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Differential-Splicing\"\u003eDifferential Splicing\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Transcript-Assembly-Visualization\"\u003eTranscript Assembly Visualization\u003c/a\u003e\u003c/li\u003e\n  \u003c/ol\u003e\n  \u003cli\u003e\u003cstrong\u003eModule 5 - Reference free analysis\u003c/strong\u003e\u003c/li\u003e\n   \u003col start=\"i\"\u003e  \n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Kallisto\"\u003eUse of Kallisto for Abundance Estimation\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_v1/wiki/Abbreviations\"\u003eAbbreviations\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Lectures\"\u003eLectures\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Solutions\"\u003ePractical Exercise Solutions\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Integrated-Assignment\"\u003eIntegrated Assignment\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/wiki/Proposed-Improvements\"\u003eProposed Improvements\u003c/a\u003e\u003c/li\u003e\n   \u003cli\u003e\u003ca href=\"https://github.com/griffithlab/rnaseq_tutorial_v1/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_v1","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgriffithlab%2Frnaseq_tutorial_v1","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Frnaseq_tutorial_v1/lists"}