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209 Stars 97 Forks GNU General Public License v3.0 227 Commits 128 Opened issues


Analysis Pipeline for Single Cell ATAC-seq

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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.

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  • Linux/Unix
  • Python (>= 2.7 & < 3.0) (SnapTools) (highly recommanded for 2.7);
  • R (>= 3.4.0 & < 3.6.0) (SnapATAC) (3.6 does not work for rhdf5 package);


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:


SnapATAC has two components: Snaptools and SnapATAC.

  • SnapTools - a python module for pre-processing and working with snap file.
  • SnapATAC - a R package for the clustering, annotation, motif discovery and downstream analysis.

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")

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