simATAC: a single-cell ATAC-seq simulation framework

• Main Authors: Zeinab Navidi, Lin Zhang, Bo Wang
• Format: Article
• Language: English
• Published: BMC 2021-03-01
• Series: Genome Biology
• Subjects: Single-cell; scATAC-seq; Simulator; Software
• Online Access: https://doi.org/10.1186/s13059-021-02270-w

Abstract Single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) identifies regulated chromatin accessibility modules at the single-cell resolution. Robust evaluation is critical to the development of scATAC-seq pipelines, which calls for reproducible datasets for benchmarking. We hereby present the simATAC framework, an R package that generates scATAC-seq count matrices that highly resemble real scATAC-seq datasets in library size, sparsity, and chromatin accessibility signals. simATAC deploys statistical models derived from analyzing 90 real scATAC-seq cell groups. simATAC provides a robust and systematic approach to generate in silico scATAC-seq samples with known cell labels for assessing analytical pipelines.