https://github.com/bowang-lab/simatac

A single-cell ATAC-seq simulation framework (R package)
https://github.com/bowang-lab/simatac

scatac-seq simulator software

Last synced: 4 days ago
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A single-cell ATAC-seq simulation framework (R package)

• Host: GitHub
• URL: https://github.com/bowang-lab/simatac
• Owner: bowang-lab
• License: gpl-3.0
• Created: 2020-07-10T14:32:44.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2021-01-23T18:39:53.000Z (almost 4 years ago)
• Last Synced: 2023-10-20T18:24:53.753Z (about 1 year ago)
• Topics: scatac-seq, simulator, software
• Language: R
• Homepage:
• Size: 19.2 MB
• Stars: 4
• Watchers: 3
• Forks: 1
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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): 

```bash

$ 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](https://github.com/bowang-lab/simATAC/blob/master/Docs/tutorial.md)

## Contact the Author

Report bugs and provide suggestions by sending email to:

Author and maintainer: Zeinab Navidi ([email protected])

Or open a new issue on this Github page.