Depth-corrected multi-factor dissection of chromatin accessibility for scATAC-seq data with PACS.

ABSTRACT: Single cell ATAC-seq (scATAC-seq) experimental designs have become increasingly complex, with multiple factors that might affect chromatin accessibility, including genotype, cell type, tissue of origin, sample location, batch, etc., whose compound effects are difficult to test by existing methods. In addition, current scATAC-seq data present statistical difficulties due to their sparsity and variations in individual sequence capture. To address these problems, we present a zero-adjusted statistical model, Probability model of Accessible Chromatin of Single cells (PACS), that allows complex hypothesis testing of accessibility-modulating factors while accounting for sparse and incomplete data. For differential accessibility analysis, PACS controls the false positive rate and achieves a 17% t

SUBMITTER: Miao Z 

PROVIDER: S-EPMC11701134 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature