CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements

Pawel F Przytycki; Katherine S Pollard

doi:10.1093/bioinformatics/btac150

CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements

Bioinformatics. 2022 Apr 28;38(9):2621-2623. doi: 10.1093/bioinformatics/btac150.

Authors

Pawel F Przytycki¹, Katherine S Pollard^{1

2

3}

Affiliations

¹ Gladstone Institutes, San Francisco, CA, USA.
² Chan Zuckerberg Biohub, San Francisco, CA, USA.
³ Department of Epidemiology and Biostatistics, Institute for Computational Health Sciences, University of California, San Francisco, CA, USA.

Abstract

Summary: CellWalkR is an R package that integrates single-cell open chromatin data with cell type labels and bulk epigenetic data to identify cell type-specific regulatory regions. A Graphics Processing Unit (GPU) implementation and downsampling strategies enable thousands of cells to be processed in seconds. CellWalkR's user-friendly interface provides interactive analysis and visualization of cell labels and regulatory region mappings.

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.

Supplementary information: Supplementary data are available at Bioinformatics online.

CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements

Authors

Affiliations

Abstract

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Grants and funding