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.
CITATION STYLE
Duren, Z., Chang, F., Naqing, F., Xin, J., Liu, Q., & Wong, W. H. (2022). Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG. Genome Biology, 23(1). https://doi.org/10.1186/s13059-022-02682-2
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