bap

Bead-based scATAC-seq data Processing

About

This is an integrated python (>= 3.6) and R package that performs analysis and identification of barcode multiplets and processes data files for downstream analyses for droplet-based single-cell ATAC-seq data.

Documentation

See the bap wiki page for details and FAQs about bap.

Installation

pip install bap-atac          # from PyPI
pip install -e .              # from a local checkout (development)

Requires Python >= 3.9. The pipeline also shells out to samtools, bedtools, R, and snakemake, which must be available on your PATH.

Testing

Automated tests use pytest. Install the test extras and run the fast suite:

pip install -e .[test]
pytest -m "not integration"   # unit + CLI smoke tests, no external tools needed
pytest                        # also runs end-to-end tests when the external tools are present

See tests/README.md for the full testing guide.