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CIRCexplorer specifications


Unique identifier OMICS_10927
Name CIRCexplorer
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Poly(A)−/ribo− RNA-seq data
Input format FASTQ,BAM
Operating system Unix/Linux
License MIT License
Computer skills Advanced
Version 1.1.3
Stability Stable
TopHat, TopHat-Fusion, STAR, bedtools, SAMtools, pysam, interval, docopt
Maintained Yes




No version available


  • person_outline Li Yang

Publication for CIRCexplorer

CIRCexplorer citations


Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjects

BMC Genomics
PMCID: 5941680
PMID: 29739336
DOI: 10.1186/s12864-018-4670-5

[…] trol brains. Over 85,000,000 reads were sequenced for each sample, with an average mapping percentage of 70.8. Using FASTQ files generated from sequencing, we ran four circRNA prediction algorithms - CIRCexplorer [], CIRI [], find_circ [], and KNIFE [], and detected a total of 4438 unique circRNAs with at least two supporting junction reads (Additional file : Table S1). Among the detected circRNA […]


Signature of circular RNAs in human induced pluripotent stem cells and derived cardiomyocytes

PMCID: 5845222
PMID: 29523209
DOI: 10.1186/s13287-018-0793-5

[…] As from hiPSCs and hiPSC-CMs (passage 30) were then subjected to RNA sequencing, and back-spliced reads in RNA-sequencing data were extracted, annotated and quantified by a combined strategy known as CIRCexplorer with default parameters, and finally scaled to RPB (reads per billion mapped reads). Only back-spliced junctions covered by at least two unique reads in a single sample were selected for […]


Improved circRNA Identification by Combining Prediction Algorithms

PMCID: 5844931
PMID: 29556495
DOI: 10.3389/fcell.2018.00020
call_split See protocol

[…] rithm, only circRNAs with at least three reads in one of the untreated samples were kept for analysis. For KNIFE, additionally, circRNAs with a posterior probability below 0.9 were discarded, and for CIRCexplorer, the circular intronic RNA (ciRNA) candidates were omitted in the subsequent analysis. Furthermore, in contrast to our previous analyses, all chrM-derived candidates were collectively rem […]


Profiling and Bioinformatic Analyses Indicate Differential circRNA and miRNA/isomiR Expression and Interactions

Biomed Res Int
PMCID: 5845524
PMID: 29682564
DOI: 10.1155/2018/8518563

[…] d qualitatively analyzed with NanoDrop (Thermo Company, USA). CircRNA and small RNA sequencing libraries were constructed with HiSeq 2000 sequencing platform following the manufacturer's instructions.CIRCexplorer software (version 1.1.7) [] was used to identify circRNAs based on the fusion gene. After trimming adaptors, the small sequence fragments were mapped onto the human genome using Bowtie [] […]


Luminal breast cancer specific circular RNAs uncovered by a novel tool for data analysis

PMCID: 5865691
PMID: 29581865
DOI: 10.18632/oncotarget.24522
call_split See protocol

[…] = 15. Gencode v19 was used as reference transcriptome dataset while hg19 as human reference genome assembly. CIRI algorithm applied in default settings with -P and -low option.CircRNA prediction with CIRCexplorer v. 1.0.6 was performed as proposed in []. RNA-Seq reads were aligned using Tophat v. 2.0.0 [] with options -bowtie1, -a = 6, -m = 2 -microexon-search -no-novel-juncs. Unmapped reads were […]


ROP: dumpster diving in RNA sequencing to find the source of 1 trillion reads across diverse adult human tissues

Genome Biol
PMCID: 5857127
PMID: 29548336
DOI: 10.1186/s13059-018-1403-7

[…] gene fusion events that are spliced across different chromosomes; and reads supporting circRNAs that are spliced in a head-to-tail configuration. To distinguish between these three categories, we use circExplorer2 (v2.0.13). CircExplorer2 relies on TopHat-Fusion (v2.0.13, bowtie1 v0.12.) and allows simultaneous monitoring of NCL events in the same run. To extract trans-spicing and gene fusion even […]


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CIRCexplorer institution(s)
Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Department of Orthopedic Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
CIRCexplorer funding source(s)
This work was supported by grants XDA01010206 and 2012OHTP08 from CAS; 2014CB964800, 2014CB910600, and 2011CBA01105 from MOST; 31322018 and 31271376 from NSFC; and 2012SSTP01 from SIBS.

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