{"id":17961226,"url":"https://github.com/erictleung/microbiome-analysis-resources","last_synced_at":"2026-01-18T06:52:29.113Z","repository":{"id":72464189,"uuid":"95603655","full_name":"erictleung/microbiome-analysis-resources","owner":"erictleung","description":":microscope: Resources and notes on studying the human microbiome","archived":false,"fork":false,"pushed_at":"2022-10-31T18:57:22.000Z","size":18,"stargazers_count":3,"open_issues_count":3,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-02-16T07:59:09.506Z","etag":null,"topics":["bioinformatics","data-analysis","gut-microbiome","microbiology","microbiome","notes","resources"],"latest_commit_sha":null,"homepage":"","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc0-1.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/erictleung.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-06-27T21:48:09.000Z","updated_at":"2024-04-23T09:23:47.000Z","dependencies_parsed_at":"2023-03-09T04:30:47.815Z","dependency_job_id":null,"html_url":"https://github.com/erictleung/microbiome-analysis-resources","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/erictleung%2Fmicrobiome-analysis-resources","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/erictleung%2Fmicrobiome-analysis-resources/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/erictleung%2Fmicrobiome-analysis-resources/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/erictleung%2Fmicrobiome-analysis-resources/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/erictleung","download_url":"https://codeload.github.com/erictleung/microbiome-analysis-resources/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247060852,"owners_count":20877158,"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":["bioinformatics","data-analysis","gut-microbiome","microbiology","microbiome","notes","resources"],"created_at":"2024-10-29T11:08:41.857Z","updated_at":"2026-01-18T06:52:29.064Z","avatar_url":"https://github.com/erictleung.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Human Microbiome Analysis Guide\n\n[![Check Resources](https://github.com/erictleung/microbiome-analysis-resources/actions/workflows/test.yml/badge.svg)](https://github.com/erictleung/microbiome-analysis-resources/actions/workflows/test.yml)\n\nGuides on analyzing the human microbiome.\n\n**Table of Contents**\n\n- [Statistical References](#statistical-references)\n- [Tutorials and Online Courses](#tutorials-and-online-courses)\n- [Software](#software)\n- [Journal Clubs](#journal-clubs)\n- [Topic and Collections](#topic-and-collections)\n- [License](#license)\n\n## Statistical References\n\n- [Guide to Statistical Analysis in Microbial Ecology (GUSTA ME)][gustame]\n- [Ordination Methods for Ecologists][ordination]\n\n[gustame]: http://mb3is.megx.net/gustame\n[ordination]: http://ordination.okstate.edu/\n\n## Tutorials and Online Courses\n\n- [Bioconductor Workflow for Microbiome Data Analysis: from raw reads to\n  community analyses][f1000]\n- [Microbiome Discovery with Dan Knights][dknights]\n- [Riffomonas Reproducible Research Tutorial Series][riff]\n- [SISMID Microbiome Data Analysis 2017][sismid2017]\n- [SISMID Microbiome Data Analysis 2018][sismid2018]\n- [Open \u0026 Reproducible Microbiome Data Analysis Spring School 2018][openmicrobiome]\n- [Amplicon Analysis - AstrobioMike][abm]\n- [Strategies and Techniques for Analyzing Microbial Population Structures\n  (STAMPS) (2019)][stamps2019]\n- [16S rRNA analysis by Rachael Lappan][16srachael]\n- [Dr. Rosen's Computational Metagenomics Special Topics Course][rosenmicro]\n\n[f1000]: http://dx.doi.org/10.12688/f1000research.8986.2\n[dknights]: https://www.youtube.com/playlist?list=PLOPiWVjg6aTzsA53N19YqJQeZpSCH9QPc\n[riff]: https://www.riffomonas.org/reproducible_research/\n[sismid2017]: http://dev-biostat.pantheonsite.io/suminst/archives/SISMID2017/MD1706\n[sismid2018]: http://www.biostat.washington.edu/suminst/archives/SISMID2018/MD1808\n[openmicrobiome]: https://mibwurrepo.github.io/Microbial-bioinformatics-introductory-course-Material-2018/introduction.html\n[abm]: https://astrobiomike.github.io/amplicon/\n[stamps2019]: https://github.com/mblstamps/stamps2019\n[16srachael]: https://rachaellappan.github.io/16S-analysis/\n[rosenmicro]: https://github.com/EESI/Comp_Metagenomics_resources\n\n## Software\n\n- [Advancing our understanding of the human microbiome using\n  QIIME][navas-molina] - Overview of the motivation for the well-known analysis\n  package, QIIME, and an entire workflow from preprocessing to diversity\n  analysis and more. Highlights 16S rRNA sequencing analysis.\n\n[navas-molina]: https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4517945\n\n## Journal Clubs\n\n- [META Center for Systems Biology][uo] - Journal club at the University of\n  Oregon Microbial Ecology and Theory of Animals (META) Center.\n- [McMaster Human Microbiome Journal Club][mcmast] - Journal club at the\n  McMaster University in Ontario, Canada.\n\n[uo]: http://meta.uoregon.edu/journal-club/\n[mcmast]: https://hmjournalclub.wordpress.com/\n\n## Topic and Collections\n\n- [Science Magazine][sciencemag]\n- [PLoS The Human Microbiome Project][ploshmp]\n- [The Microbiome and Epidemiology][annalsepi]\n\n[sciencemag]: http://www.sciencemag.org/topic/microbiome\n[ploshmp]: http://collections.plos.org/hmp\n[annalsepi]: http://www.sciencedirect.com/science/journal/10472797/26/5\n\n## License\n\n[![CC0](http://mirrors.creativecommons.org/presskit/buttons/88x31/svg/cc-zero.svg)](https://creativecommons.org/publicdomain/zero/1.0/)\n\nTo the extent possible under law, [Eric Leung](https://erictleung.com) has\nwaived all copyright and related or neighboring rights to this work.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ferictleung%2Fmicrobiome-analysis-resources","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ferictleung%2Fmicrobiome-analysis-resources","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ferictleung%2Fmicrobiome-analysis-resources/lists"}