Atac Mapper

Atac Mapper#

Tests Documentation

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

Alt text

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

  1. 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}
}
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