Atac Mapper

Map query scATAC-seq data to a single-cell chromatin accessibility atlas using cisTopics.

Getting started

Please refer to the documentation, in particular, the API documentation.

Installation

You need to have Python 3.10 or newer installed on your system. If you don't have Python installed, we recommend installing uv.

There are several alternative options to install atac_mapper:

1. Install the latest release of atac_mapper from PyPI:

pip install atac-mapper

2. Install the latest development version:

pip install git+https://github.com/quadbio/atac_mapper.git@main

Release notes

See the changelog.

Contact

For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.

Citation

If you find AtacMapper useful in your research, please, cite the following article:

@article{azbukina2025multiomic,
  title={Multi-omic human neural organoid cell atlas of the posterior brain},
  author={Azbukina, Nadezhda and He, Zhisong and Lin, Hsiu-Chuan and Santel, Malgorzata and Kashanian, Bijan and Maynard, Ashley and T{\"o}r{\"o}k, Tivadar and Okamoto, Ryoko and Nikolova, Marina and Kanton, Sabina and Br{\"o}samle, Valentin and Holtackers, Rene and Camp, J Gray and Treutlein, Barbara},
  journal={bioRxiv},
  pages={2025--03},
  year={2025},
  publisher={Cold Spring Harbor Laboratory},
  doi={10.1101/2025.03.20.644368}
}