simATAC: a single-cell ATAC-seq simulation framework

Genome Biology

Lin Zhang¹  Zeinab Navidi²  Bo Wang³ 

[1] Department of Statistical Sciences, University of Toronto, Toronto, Canada;Peter Munk Cardiac Centre, University Health Network, Toronto, Canada;Peter Munk Cardiac Centre, University Health Network, Toronto, Canada;Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada;Department of Computer Science, University of Toronto, Toronto, Canada;Vector Institute, Toronto, Canada;

关键词: Single-cell;    scATAC-seq;    Simulator;    Software;   

DOI  :  10.1186/s13059-021-02270-w

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY