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

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 i...

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Autores principales: Przytycki, Pawel F, Pollard, Katherine S
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9048661/
https://www.ncbi.nlm.nih.gov/pubmed/35274675
http://dx.doi.org/10.1093/bioinformatics/btac150
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author Przytycki, Pawel F
Pollard, Katherine S
author_facet Przytycki, Pawel F
Pollard, Katherine S
author_sort Przytycki, Pawel F
collection PubMed
description 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.
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spelling pubmed-90486612022-04-29 CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements Przytycki, Pawel F Pollard, Katherine S Bioinformatics Applications Notes 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. Oxford University Press 2022-03-11 /pmc/articles/PMC9048661/ /pubmed/35274675 http://dx.doi.org/10.1093/bioinformatics/btac150 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Przytycki, Pawel F
Pollard, Katherine S
CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements
title CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements
title_full CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements
title_fullStr CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements
title_full_unstemmed CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements
title_short CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements
title_sort cellwalkr: an r package for integrating and visualizing single-cell and bulk data to resolve regulatory elements
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9048661/
https://www.ncbi.nlm.nih.gov/pubmed/35274675
http://dx.doi.org/10.1093/bioinformatics/btac150
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