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.

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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Data Interpretation, Statistical
  • Regulatory Sequences, Nucleic Acid*
  • Software*