circRNAFinder specifications


Unique identifier OMICS_10955
Name circRNAFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Single-end RNA-seq reads. Paired-end reads should be merged into a single FASTA file.
Input format FASTA
Operating system Unix/Linux, Mac OS
Programming languages Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Bowtie, BEDTools, Integrative Genomics Viewer, FASTX-Toolkit, SRA Toolkit
Maintained Yes



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  • person_outline Fu Xing <>

circRNAFinder in publications

PMCID: 5768103
PMID: 29387208
DOI: 10.3892/ol.2017.7348

[…] rna sequencing technology combined with bioinformatics analysis may be applied to predict circrnas, and multiple circrna-associated databases have been developed for public use, including circrnafinder (), circ2traits (), find_circ (), circexplorer (), ciri (), starbase (), circnet () and circbase (). identifying more cancer-associated circrnas and evaluating their underlying […]

PMCID: 5663837
PMID: 29089539
DOI: 10.1038/s41598-017-14807-w

[…] prediction. to meet the demand of comprehensive detection of circrnas, several different pipelines with better performance in circrna analysis have been developed, including find_circ, ciri, circrnafinder, circexplorer, uroborus, etc., for further study of circrnas. however, most of existing work on circrna is based on bulk sequencing, in which individual cell properties […]

PMCID: 5680710
PMID: 27617908
DOI: 10.1080/15476286.2016.1220473

[…] topics in the field of genetics. however, the field of circular rna presents a wealth of unanswered questions. currently, several bioinformatic algorithms such as find-circ, mapsplice, circexplorer, circrnafinder and ciri are available to predict circrnas. however, the consistency of these computational tools remains relatively low, and no systematic approach is available for identifying […]

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