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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)

Features

• Preciously annotate circular RNAs (Annotate)
• Support multiple circular RNA aligners (TopHat/TopHat-Fusion, STAR, MapSplice and segemehl) (Align and Parse)
• De novo assemble novel circular RNA transcripts (Assemble)
• Characterize various of alternative splicing events of circular RNAs (Denovo)

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

Tutorial

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!

• Installation and Setup
• Pipeline
• Alignment
• Annotating
• Assembly
• Alternative Splicing

You could check FAQ for more details.

Modules

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:

• Align
• Parse
• Annotate
• Assemble
• Denovo

Related tools

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

Citation

Zhang XO*, Dong R*, Zhang Y*, Zhang JL, Luo Z, Zhang J, Chen LL#, Yang L#. Diverse alternative back-splicing and alternative splcing landscape of circular RNAs. Genome Res, 2016, doi:10.1101/gr.202895.115

License

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