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CopyscAT

Copy number variant inference with single-cell ATAC seq

INTRODUCTION CopyscAT is designed to identify large-scale and local alterations in chromosomes without need for a control file. It is currently in early beta - documentation and testing are still works in progress. Development is ongoing with R 4.0.0, so please install within an R 4.0.0 environment.

Update (Mar 2021): Now with semi-automated neoplastic vs non-neoplastic cell distinction and baseline correction (check tutorial for more details)

INSTALLATION INSTRUCTIONS To install, please download copyscat_tutorial.R and follow the instructions within. To generate fragment matrices, use the process_fragment_file.py script (type python3 process_fragment_file.py for details regarding input parameters)


Copyright (C) 2020 University of Calgary

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

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Inferring CNV data from single cell ATAC seq

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