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

CIRCexplorer2 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)

NEWS:

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.

CLEAR is a newly developped pipeline compatible with CIRCexplorer2 to help better quantify and compare the expression of circRNAs. (Ma et al., 2020)

CIRCpedia is an integrative database, aiming to annotating alternative back-splicing and alternative splicing in circRNAs across different cell lines. Welcome to use! (Dong et al., 2018)

Features

  • Precisely annotate circular RNAs with high accuracy, good sensitivity and low memory consumption [1][2][3]
  • Support multiple circular RNA aligners (TopHat2/TopHat-Fusion, STAR, MapSplice, BWA and segemehl)
  • De novo assemble novel circular RNA transcripts
  • Characterize various of alternative (back-)splicing events of circular RNAs
  • Fast identify circuar RNAs with STAR or BWA
  • Support both single-read and paired-end sequencing.

CIRCexplorer2 documentation is available through https://readthedocs.org/ from here, including installation instructions and tutorial.

Protocol: Dong R, Ma XK, Chen LL, Yang L#. Genome-Wide annotation of circRNAs and their alternative back-splicing/splicing with CIRCexplorer pipeline. Methods Mol Biol, 2019, 1870:137-149 (Book chapter)

Citation

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

License

Copyright (C) 2016-2019 YangLab. See the LICENSE file for license rights and limitations (MIT).