https://github.com/gersteinlab/scan-atac-sim
SCAN-ATAC Sim is a single-cell ATAC-seq data simulator used to benchmark various single-cell ATAC-seq data analysis methods.
https://github.com/gersteinlab/scan-atac-sim
Last synced: 2 months ago
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SCAN-ATAC Sim is a single-cell ATAC-seq data simulator used to benchmark various single-cell ATAC-seq data analysis methods.
- Host: GitHub
- URL: https://github.com/gersteinlab/scan-atac-sim
- Owner: gersteinlab
- Created: 2020-12-10T05:28:29.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2020-12-10T05:39:18.000Z (over 4 years ago)
- Last Synced: 2025-01-20T12:07:46.647Z (4 months ago)
- Language: C++
- Size: 630 KB
- Stars: 1
- Watchers: 14
- Forks: 0
- Open Issues: 1
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Metadata Files:
- Readme: README.md
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README
# SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments
scATAC-seq is a powerful approach for characterizing cell-type-specific regulatory landscapes. However, it is difficult to benchmark the performance of various scATAC-seq analysis techniques (such as clustering and deconvolution) without having a priori a known set of gold-standard cell types. To simulate scATAC-seq experiments with known cell-type labels, we introduce an efficient and scalable scATAC-seq simulation method (SCAN-ATAC-Sim) that down-samples bulk ATAC-seq data (e.g. from representative cell lines or tissues). Our protocol uses a consistent but tunable signal-to-noise ratio across cell types in a scATAC-seq simulation for integrating bulk experiments with different levels of background noise, and it independently samples twice without replacement to account for the diploid genome. Because it uses an efficient weighted reservoir sampling algorithm and is highly parallelizable with OpenMP, our implementation in C++ allows millions of cells to be simulated in less than an hour on a laptop computer.