Cargando…
ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulato...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group US
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8012210/ https://www.ncbi.nlm.nih.gov/pubmed/33633365 http://dx.doi.org/10.1038/s41588-021-00790-6 |
_version_ | 1783673334629662720 |
---|---|
author | Granja, Jeffrey M. Corces, M. Ryan Pierce, Sarah E. Bagdatli, S. Tansu Choudhry, Hani Chang, Howard Y. Greenleaf, William J. |
author_facet | Granja, Jeffrey M. Corces, M. Ryan Pierce, Sarah E. Bagdatli, S. Tansu Choudhry, Hani Chang, Howard Y. Greenleaf, William J. |
author_sort | Granja, Jeffrey M. |
collection | PubMed |
description | The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; https://www.archrproject.com/) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses, including doublet removal, single-cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing (scRNA-seq). Enabling the analysis of over 1.2 million single cells within 8 h on a standard Unix laptop, ArchR is a comprehensive software suite for end-to-end analysis of single-cell chromatin accessibility that will accelerate the understanding of gene regulation at the resolution of individual cells. |
format | Online Article Text |
id | pubmed-8012210 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group US |
record_format | MEDLINE/PubMed |
spelling | pubmed-80122102021-04-16 ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis Granja, Jeffrey M. Corces, M. Ryan Pierce, Sarah E. Bagdatli, S. Tansu Choudhry, Hani Chang, Howard Y. Greenleaf, William J. Nat Genet Technical Report The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; https://www.archrproject.com/) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses, including doublet removal, single-cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing (scRNA-seq). Enabling the analysis of over 1.2 million single cells within 8 h on a standard Unix laptop, ArchR is a comprehensive software suite for end-to-end analysis of single-cell chromatin accessibility that will accelerate the understanding of gene regulation at the resolution of individual cells. Nature Publishing Group US 2021-02-25 2021 /pmc/articles/PMC8012210/ /pubmed/33633365 http://dx.doi.org/10.1038/s41588-021-00790-6 Text en © The Author(s), under exclusive licence to Springer Nature America, Inc. 2021, corrected publication 2021 https://creativecommons.org/licenses/by/4.0/Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Technical Report Granja, Jeffrey M. Corces, M. Ryan Pierce, Sarah E. Bagdatli, S. Tansu Choudhry, Hani Chang, Howard Y. Greenleaf, William J. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis |
title | ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis |
title_full | ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis |
title_fullStr | ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis |
title_full_unstemmed | ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis |
title_short | ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis |
title_sort | archr is a scalable software package for integrative single-cell chromatin accessibility analysis |
topic | Technical Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8012210/ https://www.ncbi.nlm.nih.gov/pubmed/33633365 http://dx.doi.org/10.1038/s41588-021-00790-6 |
work_keys_str_mv | AT granjajeffreym archrisascalablesoftwarepackageforintegrativesinglecellchromatinaccessibilityanalysis AT corcesmryan archrisascalablesoftwarepackageforintegrativesinglecellchromatinaccessibilityanalysis AT piercesarahe archrisascalablesoftwarepackageforintegrativesinglecellchromatinaccessibilityanalysis AT bagdatlistansu archrisascalablesoftwarepackageforintegrativesinglecellchromatinaccessibilityanalysis AT choudhryhani archrisascalablesoftwarepackageforintegrativesinglecellchromatinaccessibilityanalysis AT changhowardy archrisascalablesoftwarepackageforintegrativesinglecellchromatinaccessibilityanalysis AT greenleafwilliamj archrisascalablesoftwarepackageforintegrativesinglecellchromatinaccessibilityanalysis |