CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues.

ABSTRACT: Single-cell and bulk genomics assays have complementary strengths and weaknesses, and alone neither strategy can fully capture regulatory elements across the diversity of cells in complex tissues. We present CellWalker, a method that integrates single-cell open chromatin (scATAC-seq) data with gene expression (RNA-seq) and other data types using a network model that simultaneously improves cell labeling in noisy scATAC-seq and annotates cell type-specific regulatory elements in bulk data. We demonstrate CellWalker's robustness to sparse annotations and noise using simulations and combined RNA-seq and ATAC-seq in individual cells. We then apply CellWalker to the developing brain. We identify cells transitioning between transcriptional states, resolve regulatory elements to cell types, and o

SUBMITTER: Przytycki PF 

PROVIDER: S-EPMC7883575 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature