https://github.com/databio/pepatac
A modular, containerized pipeline for ATAC-seq data processing
https://github.com/databio/pepatac
Last synced: 9 months ago
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A modular, containerized pipeline for ATAC-seq data processing
- Host: GitHub
- URL: https://github.com/databio/pepatac
- Owner: databio
- License: bsd-2-clause
- Created: 2016-05-12T21:29:13.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2025-09-23T17:08:02.000Z (9 months ago)
- Last Synced: 2025-09-23T19:09:47.478Z (9 months ago)
- Language: Python
- Homepage: http://pepatac.databio.org
- Size: 21.9 MB
- Stars: 59
- Watchers: 21
- Forks: 16
- Open Issues: 55
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
---
[](http://pepkit.github.io)
PEPATAC is a pipeline for ATAC-seq data. For more information see: http://pepatac.databio.org/
## Docs
Develop docs with:
```
mkdocs serve -f mkdocs.yml
```
Build and deploy with:
```
mkdocs build -f mkdocs.yml -d $CODEBASE/code.databio.org/pepatac/
```
## Contributing
Pull requests welcome. Active development should occur in a development or feature branch.
## Contributors
* Jason Smith, jasonsmith@virginia.edu
* Nathan Sheffield, nathan@code.databio.org
* Jin Xu, jinxu9@stanford.edu
* Ryan Corces, rcorces@stanford.edu
* Vince Reuter, vreuter@protonmail.com
* Donald Campbell, https://github.com/donaldcampbelljr
* Others... (add your name)
## Citing
If you find PEPATAC useful in your research, please cite:
Jason P. Smith, M. Ryan Corces, Jin Xu, Vincent P. Reuter, Howard Y. Chang, and Nathan C. Sheffield. PEPATAC: An optimized ATAC-seq pipeline with serial alignments. bioRxiv (2021). DOI: 10.1101/2020.10.21.347054