scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data

Single-cell chromatin accessibility sequencing has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. However, there is a lack of open-source software for comprehensive processing, analysis, and visualization of such data generated using all existing experime...

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Autores principales: Yu, Wenbao, Uzun, Yasin, Zhu, Qin, Chen, Changya, Tan, Kai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169039/
https://www.ncbi.nlm.nih.gov/pubmed/32312293
http://dx.doi.org/10.1186/s13059-020-02008-0
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author Yu, Wenbao
Uzun, Yasin
Zhu, Qin
Chen, Changya
Tan, Kai
author_facet Yu, Wenbao
Uzun, Yasin
Zhu, Qin
Chen, Changya
Tan, Kai
author_sort Yu, Wenbao
collection PubMed
description Single-cell chromatin accessibility sequencing has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. However, there is a lack of open-source software for comprehensive processing, analysis, and visualization of such data generated using all existing experimental protocols. Here, we present scATAC-pro for quality assessment, analysis, and visualization of single-cell chromatin accessibility sequencing data. scATAC-pro computes a range of quality control metrics for several key steps of experimental protocols, with a flexible choice of methods. It generates summary reports for both quality assessment and downstream analysis. scATAC-pro is available at https://github.com/tanlabcode/scATAC-pro.
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spelling pubmed-71690392020-04-23 scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data Yu, Wenbao Uzun, Yasin Zhu, Qin Chen, Changya Tan, Kai Genome Biol Software Single-cell chromatin accessibility sequencing has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. However, there is a lack of open-source software for comprehensive processing, analysis, and visualization of such data generated using all existing experimental protocols. Here, we present scATAC-pro for quality assessment, analysis, and visualization of single-cell chromatin accessibility sequencing data. scATAC-pro computes a range of quality control metrics for several key steps of experimental protocols, with a flexible choice of methods. It generates summary reports for both quality assessment and downstream analysis. scATAC-pro is available at https://github.com/tanlabcode/scATAC-pro. BioMed Central 2020-04-20 /pmc/articles/PMC7169039/ /pubmed/32312293 http://dx.doi.org/10.1186/s13059-020-02008-0 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Yu, Wenbao
Uzun, Yasin
Zhu, Qin
Chen, Changya
Tan, Kai
scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
title scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
title_full scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
title_fullStr scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
title_full_unstemmed scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
title_short scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
title_sort scatac-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169039/
https://www.ncbi.nlm.nih.gov/pubmed/32312293
http://dx.doi.org/10.1186/s13059-020-02008-0
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