simATAC: a single-cell ATAC-seq simulation framework

simATAC is a framework provided as an R package that generates a single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) count matrix, highly resembling real scATAC-seq datasets in library size, sparsity, and averaged chromatin accessibility signals. simATAC deploys statistical functions derived from analyzing 90 real scATAC-seq cell groups to model read distributions. simATAC provides a robust and systematic approach to generate in silico scATAC-seq samples with cell labels for a comprehensive tool assessment.

Installation

Install simATAC R package (R >= 3.5.0):

$ R
> library(devtools)
> install_github("bowang-lab/simATAC")

Getting started

simATAC tutorial provides examples and explanations of its functions and how to use them. This documentation introduces the main features of simATAC.

• simATAC tutorial

Contact the Author

Report bugs and provide suggestions by sending email to:

Author and maintainer: Zeinab Navidi (zeinab.nvd@gmail.com)

Or open a new issue on this Github page.