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https://github.com/erictleung/microbiome-analysis-resources
:microscope: Resources and notes on studying the human microbiome
https://github.com/erictleung/microbiome-analysis-resources
bioinformatics data-analysis gut-microbiome microbiology microbiome notes resources
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:microscope: Resources and notes on studying the human microbiome
- Host: GitHub
- URL: https://github.com/erictleung/microbiome-analysis-resources
- Owner: erictleung
- License: cc0-1.0
- Created: 2017-06-27T21:48:09.000Z (over 7 years ago)
- Default Branch: main
- Last Pushed: 2022-10-31T18:57:22.000Z (about 2 years ago)
- Last Synced: 2024-06-11T23:04:51.696Z (7 months ago)
- Topics: bioinformatics, data-analysis, gut-microbiome, microbiology, microbiome, notes, resources
- Homepage:
- Size: 17.6 KB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Human Microbiome Analysis Guide
[](https://github.com/erictleung/microbiome-analysis-resources/actions/workflows/test.yml)
Guides on analyzing the human microbiome.
**Table of Contents**
- [Statistical References](#statistical-references)
- [Tutorials and Online Courses](#tutorials-and-online-courses)
- [Software](#software)
- [Journal Clubs](#journal-clubs)
- [Topic and Collections](#topic-and-collections)
- [License](#license)
## Statistical References
- [Guide to Statistical Analysis in Microbial Ecology (GUSTA ME)][gustame]
- [Ordination Methods for Ecologists][ordination]
[gustame]: http://mb3is.megx.net/gustame
[ordination]: http://ordination.okstate.edu/
## Tutorials and Online Courses
- [Bioconductor Workflow for Microbiome Data Analysis: from raw reads to
community analyses][f1000]
- [Microbiome Discovery with Dan Knights][dknights]
- [Riffomonas Reproducible Research Tutorial Series][riff]
- [SISMID Microbiome Data Analysis 2017][sismid2017]
- [SISMID Microbiome Data Analysis 2018][sismid2018]
- [Open & Reproducible Microbiome Data Analysis Spring School 2018][openmicrobiome]
- [Amplicon Analysis - AstrobioMike][abm]
- [Strategies and Techniques for Analyzing Microbial Population Structures
(STAMPS) (2019)][stamps2019]
- [16S rRNA analysis by Rachael Lappan][16srachael]
- [Dr. Rosen's Computational Metagenomics Special Topics Course][rosenmicro]
[f1000]: http://dx.doi.org/10.12688/f1000research.8986.2
[dknights]: https://www.youtube.com/playlist?list=PLOPiWVjg6aTzsA53N19YqJQeZpSCH9QPc
[riff]: https://www.riffomonas.org/reproducible_research/
[sismid2017]: http://dev-biostat.pantheonsite.io/suminst/archives/SISMID2017/MD1706
[sismid2018]: http://www.biostat.washington.edu/suminst/archives/SISMID2018/MD1808
[openmicrobiome]: https://mibwurrepo.github.io/Microbial-bioinformatics-introductory-course-Material-2018/introduction.html
[abm]: https://astrobiomike.github.io/amplicon/
[stamps2019]: https://github.com/mblstamps/stamps2019
[16srachael]: https://rachaellappan.github.io/16S-analysis/
[rosenmicro]: https://github.com/EESI/Comp_Metagenomics_resources
## Software
- [Advancing our understanding of the human microbiome using
QIIME][navas-molina] - Overview of the motivation for the well-known analysis
package, QIIME, and an entire workflow from preprocessing to diversity
analysis and more. Highlights 16S rRNA sequencing analysis.
[navas-molina]: https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4517945
## Journal Clubs
- [META Center for Systems Biology][uo] - Journal club at the University of
Oregon Microbial Ecology and Theory of Animals (META) Center.
- [McMaster Human Microbiome Journal Club][mcmast] - Journal club at the
McMaster University in Ontario, Canada.
[uo]: http://meta.uoregon.edu/journal-club/
[mcmast]: https://hmjournalclub.wordpress.com/
## Topic and Collections
- [Science Magazine][sciencemag]
- [PLoS The Human Microbiome Project][ploshmp]
- [The Microbiome and Epidemiology][annalsepi]
[sciencemag]: http://www.sciencemag.org/topic/microbiome
[ploshmp]: http://collections.plos.org/hmp
[annalsepi]: http://www.sciencedirect.com/science/journal/10472797/26/5
## License
[](https://creativecommons.org/publicdomain/zero/1.0/)
To the extent possible under law, [Eric Leung](https://erictleung.com) has
waived all copyright and related or neighboring rights to this work.