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.
1 maintainer
Metadata
1 maintainer
Release files for ATACofthesnake 0.14.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| atacofthesnake-0.14.1.tar.gz | 985.3 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| atacofthesnake-0.14.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 1.0 MB
Release files / atacofthesnake-0.14.1.tar.gz
| Download URL | atacofthesnake-0.14.1.tar.gz |
|---|---|
| Size | 985.3 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
938ba2bfa0d142cc478d77ab15c5c3ff0a935f5f8137ccddacaeb22128b017b2
|
|
BLAKE2b-256 checksum How to use checksums |
3b62e0737f9ab8a0e9ebd62854f33ae0d66d8aff45454d6eb850f57e4b350e5a
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.14.7
|
Release files / atacofthesnake-0.14.1-py3-none-any.whl
| Download URL | atacofthesnake-0.14.1-py3-none-any.whl |
|---|---|
| Size | 52.7 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
55b955f49d6e1b91d691d7628f1fd473ddfdad45581b863d312012e0faae903a
|
|
BLAKE2b-256 checksum How to use checksums |
1da0111b23bcb4390494bac9c29e5e0c1c10e49bcd2661994d86a8fb0e5c46a8
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.14.7
|
