https://github.com/maxplanck-ie/atacofthesnake

Differential accessibility, LRT tests and timecourse analyses for chromatin accessibility data
https://github.com/maxplanck-ie/atacofthesnake

atac atac-seq atacseq gaussian-processes lrt multifactor time-course timecourse-analysis

Last synced: 3 days ago
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Differential accessibility, LRT tests and timecourse analyses for chromatin accessibility data

• Host: GitHub
• URL: https://github.com/maxplanck-ie/atacofthesnake
• Owner: maxplanck-ie
• License: mit
• Created: 2020-12-22T13:33:36.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2026-06-09T10:04:17.000Z (3 days ago)
• Last Synced: 2026-06-09T11:10:28.817Z (3 days ago)
• Topics: atac, atac-seq, atacseq, gaussian-processes, lrt, multifactor, time-course, timecourse-analysis
• Language: Python
• Homepage: https://atacofthesnake.readthedocs.io/en/latest/
• Size: 1.18 MB
• Stars: 4
• Watchers: 2
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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README

          

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# ATACofthesnake

Downstream processing of ATAC data, including QC, differential accessibility -, LRT - and timecourse analyses. Optional downstream motif analyses included.

Starting point are deduplicated BAM and/or CRAM files.

## Important

All samples in a 'run' have to belong to the same group. That means that out of all peaks/sample, a union will be made. In case this is not the case, you can run the workflow multiple times.

Fasta headers are not allowed to contain a pipe character '|' (as peaks will be delimited as such later on).

## Installation

From pypi:

>  pip install ATACofthesnake  

or with uv:

>  uv pip install ATACofthesnake  

From github:

>  git clone git@github.com:maxplanck-ie/ATACofthesnake.git  

>  pixi run ATAC -h  

## Quickstart

 > ATAC -h

Bare minimum needed input:

 - directory with deduplicated bam and/or cram files.  

 - genome fasta file  

 - genome annotation file (GTF format)  

 - read attracting regions (BED format), this is necessary and needs to contain at least the full mitochondrial chromosome.  

For more details and how-to on requesting specific differential analysis and comparisons, please refer to the [documentation](https://atacofthesnake.readthedocs.io/en/stable/).