Abstract
While single-cell open chromatin (scATAC-seq) data allows for the identification of cell type-specific regulatory regions, it is much sparser than bulk data. CellWalkR is an R package that performs an integration of external labeling and bulk epigenetic data with scATAC-seq using a network-based random walk model to help overcome this sparsity. Outputs include cell type labels for individual cells and regulatory regions.
Availability and implementation CellWalkR is freely available as an R package under a GNU GPL-2.0 License, and can be accessed from https://github.com/PFPrzytycki/CellWalkR with an accompanying vignette for analyzing example data.
Competing Interest Statement
The authors have declared no competing interest.
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.