Home

Awesome

SnapATAC (Latest Updates: 2019-09-19)

SnapATAC (Single Nucleus Analysis Pipeline for ATAC-seq) is a fast, accurate and comprehensive method for analyzing single cell ATAC-seq datasets.

Please find the latest version SnapATAC (2.0) by the following link: https://github.com/kaizhang/SnapATAC2

Latest News

FAQs

Requirements

Pre-print

Rongxin Fang, Sebastian Preissl, Xiaomeng Hou, Jacinta Lucero, Xinxin Wang, Amir Motamedi, Andrew K. Shiau, Eran A. Mukamel, Yanxiao Zhang, M. Margarita Behrens, Joseph Ecker, Bing Ren. Fast and Accurate Clustering of Single Cell Epigenomes Reveals Cis-Regulatory Elements in Rare Cell Types. bioRxiv 615179; doi: https://doi.org/10.1101/615179

Installation

SnapATAC has two components: Snaptools and SnapATAC.

Install snaptools from PyPI. See how to install snaptools on FAQs. NOTE: Please use python 2.7 if possible.

$ pip install snaptools

Install SnapATAC R pakcage (development version).

$ R
> library(devtools)
> install_github("r3fang/SnapATAC")

Galleries & Tutorials (click on the image for details)

<img src="./images/10X_brain_5k.png" width="280" height="318" /> <img src="./images/PBMC_ATAC_RNA.png" width="280" height="318" /> <img src="./images/10X_snATAC.png" width="280" height="318" />