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SimATAC: a single-cell ATAC-seq simulation framework.

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.

SUBMITTER: Navidi Z

PROVIDER: S-EPMC7934446 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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simATAC: a single-cell ATAC-seq simulation framework.

Navidi Zeinab Z Zhang Lin L Wang Bo B

Genome biology 20210304 1

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. si ...[more]

PMID: 33663563

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