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Build Status Coverage Status Documentation Status PyPI install with bioconda Anaconda-Server Downloads The MIT License

CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization.

Authors: Xiao-Ou Zhang (zhangxiaoou@picb.ac.cn), Li Yang (liyang@picb.ac.cn)

Maintainer: Xu-Kai Ma (maxukai@picb.ac.cn)


From version 2.3.0, CIRCexplorer2 has very big changes in inputs and outputs. For new structures, please see http://circexplorer2.readthedocs.org. If you want to check the information for old versions, please see http://circexplorer2.readthedocs.io/en/2.2.7 .

CIRCpedia is an integrative database, aiming to annotating alternative back-splicing and alternative splicing in circRNAs across different cell lines. Welcome to use!


  • Precisely annotate circular RNAs (Annotate)
  • Support multiple circular RNA aligners (TopHat2/TopHat-Fusion, STAR, MapSplice, BWA and segemehl) (Align and Parse)
  • De novo assemble novel circular RNA transcripts (Assemble)
  • Characterize various of alternative (back-)splicing events of circular RNAs (Denovo)
  • Fast identify circuar RNAs with STAR or BWA (Parse)
  • Support both single-read and paired-end sequencing.

For some frequently asked questions about CIRCexplorer2, please FAQ for more details.


We have developed a fairly comprehensive tutorial that demonstrates how CIRCexplorer2 helps you to promote your research in circular RNA identification and characterization. Please check it below!

We also offered fast_circ.py script to help you to automatically run our pipelines in one step without any additional operations. Please check this one-step script for more details.


CIRCexplorer2 contains 5 modules. Each module functions as an independent component owning its distinctive duty. Meanwhile, they inteact with each other, and different circular RNA analysis pipelines are derived from different combinations of several modules. Understanding the detailed mechanism of each module could facilitate your circular RNA research.

List of Modules:

We developed a series of circular RNA analysis tools, and welcome to use and cite our work. See Related Tools for more information.


Zhang XO*, Dong R*, Zhang Y*, Zhang JL, Luo Z, Zhang J, Chen LL#, Yang L#. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res, 2016, 26:1277-1287


Copyright (C) 2016-2017 YangLab. See LICENSE for license rights and limitations (MIT).