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Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
- Source :
- Genome Biology, Vol 23, Iss 1, Pp 1-19 (2022)
- Publication Year :
- 2022
- Publisher :
- BMC, 2022.
-
Abstract
- Abstract Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory potential, for single cell multiome data. This concept is further used for the construction of subpopulation-specific cis-regulatory networks. The capability of inferring useful regulatory network is demonstrated by the two-fold increment on network inference accuracy compared to the Pearson correlation-based method and the 27-fold enrichment of GWAS variants for inflammatory bowel disease in the cis-regulatory elements. The R package scREG provides comprehensive functions for single cell multiome data analysis.
Details
- Language :
- English
- ISSN :
- 1474760X
- Volume :
- 23
- Issue :
- 1
- Database :
- Directory of Open Access Journals
- Journal :
- Genome Biology
- Publication Type :
- Academic Journal
- Accession number :
- edsdoj.9b3eb985cb248bd9ae1d1674c46c815
- Document Type :
- article
- Full Text :
- https://doi.org/10.1186/s13059-022-02682-2