SnapATAC is a software package for analyzing scATAC-seq datasets. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states.

References:

• Rongxin Fang, Sebastian Preissl, Yang Li, Xiaomeng Hou, Jacinta Lucero, Xinxin Wang, Amir Motamedi, Andrew K. Shiau, Xinzhu Zhou, Fangming Xie, Eran A. Mukamel, Kai Zhang, Yanxiao Zhang, M. Margarita Behrens, Joseph R. Ecker & Bing Ren
  Comprehensive analysis of single cell ATAC-seq data with SnapATAC
  NATURE COMMUNICATIONS | (2021) 12:1337 | https://doi.org/10.1038/s41467-021-21583-9 | www.nature.com/naturecommunications,
  

• SnapATAC2 Github page
• SnapATAC2 Tutiorials

• Module Name: SnapATAC2 (see the modules page for more information)
• Unusual environment variables set
  • SNAPATAC2_HOME   installation directory
  • SNAPATAC2_BIN         executable directory
  • SNAPATAC2_SRC     test data directory
  • SNAPATAC2_TESTS     test scripts folder

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn4199 ~]$ module load SnapATAC2
[+] Loading singularity  3.10.3  on cn4199
[+] Loading SnapATAC2 2.1.2  ...

[user@cn4199 ~]$ python $SNAPATAC2_TESTS/test_func.py
[user@cn4199 ~]$ python $SNAPATAC2_TESTS/test_pickle.py
[user@cn4199 ~]$ python $SNAPATAC2_TESTS/test_similarity.py
[user@cn4199 ~]$ python $SNAPATAC2_TESTS/test_tools.py

[user@cn4199 ~]$ python
Python 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:53)
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import snapatac2 as snap
>>> snap.__version__
'2.1.2'