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)
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