epiAneufinder is an algorithm used for calling Copy Number Variations (CNVs) from single-cell ATAC (scATAC) data. Single-cell open chromatin profiling via the single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) assay has become a mainstream measurement of open chromatin in single-cells. epiAneufinder exploits the read count information from scATAC-seq data to extract genome-wide copy number variations (CNVs) for each individual cell. epiAneufinder allows the addition of single-cell CNV information to scATAC-seq data, without the need of additional experiments, unlocking a layer of genomic variation which is otherwise unexplored.
Ramakrishnan, A., Symeonidi, A., Hanel, P. et al. epiAneufinder identifies copy number alterations from single-cell ATAC-seq data. Nat Commun 14, 5846 (2023). https://doi.org/10.1038/s41467-023-41076-1
The algorithm can be found here https://github.com/colomemaria/epiAneufinder
The repository contains the scripts that were used for the analyses of the differnt datasets presented in the epiAneufinder publication.
Contributors names and contact info
Akshaya Ramakrishnan (akshaya4r@gmail.com)
Aikaterini Symeonidi (aikaterini.symeonidi@helmholtz-muenchen.de)
Patrick Hanel (patrick.hanel@helmholtz-muenchen.de)
Katharina Schmid (katharina.schmid@bmc.med.lmu.de)
Maria Richter (maria.richter@bmc.med.lmu.de)
Michael Schubert
Maria Colomé-Tatché (maria.colome@helmholtz-muenchen.de)
This project is licensed under the GNU General Public License v3.0 - see the LICENSE.md file for details
