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