pyEpiAneufinder 0.3.6

Identify copy number variations from single-cell ATAC-seq data

pyEpiAneufinder: Identifying copy number alterations from single-cell ATAC-seq data

This package is the Python re-implementation of our R package epiAneufinder, developed for identifying copy number variations (CNVs) from single-cell ATAC-seq data.

Important remark: The Python package is still in beta testing. Please report issues and improvement suggestions through GitHub Issues.

Single-cell open chromatin profiling through scATAC-seq provides fragment count information that can be used to infer copy number variation. pyEpiAneufinder uses this information to extract genome-wide CNV profiles for individual cells, adding a layer of genomic variation analysis without requiring additional experiments.

The original epiAneufinder publication is:

Ramakrishnan, A., Symeonidi, A., Hanel, P. et al. epiAneufinder identifies copy number alterations from single-cell ATAC-seq data. Nature Communications 14, 5846 (2023). https://doi.org/10.1038/s41467-023-41076-1

The R version, including additional background information, is available at: https://github.com/colomemaria/epiAneufinder

Installation

pip install pyEpiAneufinder

For development, including tests and docs:

pip install -e ".[test,docs]"

The full workflow guide, figures, API usage, and example analyses are available in the Read the Docs documentation: https://pyepianeufinder.readthedocs.io/

Cite

If you use pyEpiAneufinder, please cite both the package and the original epiAneufinder publication.

Package / repository:

Schmid, K., Symeonidi, A., Nikolaou, A., Bueschel, I., and Colome-Tatche, M. pyEpiAneufinder. GitHub repository: https://github.com/macelik/pyEpiAneufinder

Original method paper:

Ramakrishnan, A., Symeonidi, A., Hanel, P. et al. epiAneufinder identifies copy number alterations from single-cell ATAC-seq data. Nature Communications 14, 5846 (2023). https://doi.org/10.1038/s41467-023-41076-1

Authors of the Python Re-implementation

Katharina Schmid ([e-mail])

Aikaterini Symeonidi ([e-mail] and [e-mail])

Angelos Nikolaou ([e-mail])

Ida Bueschel ([e-mail])

Maria Colome-Tatche ([e-mail])

Version history

• 0.3.6
  • Test release for GitHub Release and PyPI publishing workflows
• 0.1
  • Initial Release (based on epiAneufinder v1.1.3)