# CIRCexplorer2

**Repository Path**: Si-Nan/CIRCexplorer2

## Basic Information

- **Project Name**: CIRCexplorer2
- **Description**: circular RNA analysis toolset
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 1
- **Forks**: 0
- **Created**: 2022-01-24
- **Last Updated**: 2025-03-13

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

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CIRCexplorer2 is the successor of [CIRCexplorer](http://yanglab.github.io/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](https://github.com/YangLab/CLEAR) is a newly developped pipeline compatible with CIRCexplorer2 to help better quantify and compare the expression of circRNAs. [(Ma et al., 2020)](https://www.sciencedirect.com/science/article/pii/S1672022919301664)

[CIRCpedia](http://www.picb.ac.cn/rnomics/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)](https://www.sciencedirect.com/science/article/pii/S1672022918302596)

## Features

* Precisely annotate circular RNAs with high accuracy, good sensitivity and low memory consumption [[1](http://nar.oxfordjournals.org/content/44/6/e58.abstract)][[2](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005420)][[3](https://www.frontiersin.org/articles/10.3389/fcell.2018.00020/full)]
* 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](http://CIRCexplorer2.readthedocs.org), 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)](https://link.springer.com/protocol/10.1007/978-1-4939-8808-2_10)

## 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](http://genome.cshlp.org/content/26/9/1277.abstract)

## License

Copyright (C) 2016-2019 YangLab.  See the [LICENSE](https://github.com/YangLab/CIRCexplorer2/blob/master/LICENSE.txt)
file for license rights and limitations (MIT).