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ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis.
Jeffrey M Granja1,2,3, M Ryan Corces4,5,6,7, Sarah E Pierce8,9
1Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. jgranja.stanford@gmail.com.
Nature Genetics
|February 26, 2021
Summary
ArchR is a new software suite for analyzing single-cell chromatin accessibility data. This tool enables fast, comprehensive insights into gene regulation at the single-cell level.
Area of Science:
- Genomics
- Computational Biology
- Epigenetics
Background:
- Single-cell chromatin accessibility profiling advances gene regulatory landscape mapping.
- Software development for analyzing this data has lagged behind experimental capabilities.
Purpose of the Study:
- To introduce ArchR, a software suite for rapid and comprehensive analysis of single-cell chromatin accessibility data.
- To provide an intuitive platform for complex single-cell analyses.
Main Methods:
- ArchR software suite developed in R.
- Utilizes single-cell chromatin accessibility data.
- Incorporates algorithms for doublet removal, clustering, cell type identification, peak generation, trajectory analysis, gene linkage, transcription factor footprinting, and multi-omic integration.
Main Results:
- ArchR enables fast and comprehensive analysis of single-cell chromatin accessibility data.
- Supports complex analyses including cell type identification and trajectory inference.
- Scalable to over 1.2 million cells analyzed within 8 hours on a standard laptop.
Conclusions:
- ArchR accelerates understanding of gene regulation at single-cell resolution.
- Provides an end-to-end solution for single-cell chromatin accessibility data analysis.
- Facilitates multi-omic integration with single-cell RNA sequencing.
