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bioRxiv · 10.1101/2020.08.14.251488

simATAC: A Single-cell ATAC-seq Simulation Framework

Navidi Ghaziani, Z.·Zhang, L.·Wang, B.
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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.

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Navidi Ghaziani, Z., Zhang, L., Wang, B.. 2020-08-14. simATAC: A Single-cell ATAC-seq Simulation Framework. https://doi.org/10.1101/2020.08.14.251488

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