RT Journal Article
SR Electronic
T1 scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 824326
DO 10.1101/824326
A1 Wenbao Yu
A1 Yasin Uzun
A1 Qin Zhu
A1 Changya Chen
A1 Kai Tan
YR 2019
UL http://biorxiv.org/content/early/2019/10/30/824326.abstract
AB Single cell chromatin accessibility sequencing (scCAS) has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. A number of experimental protocols have been developed for scCAS. However, there is a lack of flexible and open-source software tools for comprehensive processing, analysis and visualization of scCAS data generated using all existing experimental protocols. Here we present scATAC-pro for processing, analyzing and visualization of scCAS data. scATAC-pro provides flexible choice of methods for different data processing and analytical tasks, with carefully curated default parameters. scATAC-pro also generates detailed data quality and analysis reports in html format and provides interface to visualization software and additional utility functions for various types of downstream analyses.