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Citations per year

Number of citations per year for the bioinformatics software tool Piranha

Tool usage distribution map

This map represents all the scientific publications referring to Piranha per scientific context
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Piranha specifications


Unique identifier OMICS_00568
Name Piranha
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2.1
Stability Stable
GNU scientific, BAMtools, GCC
Maintained Yes




No version available


  • person_outline Andrew Smith

Publication for Piranha

Piranha citations


CLIP related methodologies and their application to retrovirology

PMCID: 5930818
PMID: 29716635
DOI: 10.1186/s12977-018-0417-2

[…] of whether a binding event is merely a result of transcript abundance or a more specific interaction between the RBP and its target RNA. Several peak calling programs have been developed and include Piranha [], CLIPper [], PIPE-CLIP [], Pyicos [] that work with all CLIP variants, and PARalyzer [] and wavClusteR that are specifically developed for PAR-CLIP analysis. For more details on the statist […]


Distinct and Modular Organization of Protein Interacting Sites in Long Non coding RNAs

Front Mol Biosci
PMCID: 5893854
PMID: 29670884
DOI: 10.3389/fmolb.2018.00027

[…] s and is known to be localized in nucleus. We plotted the binding sites for all RBPs to the full-length of MALAT1 transcripts and the same is shown in Figure for ClipDB-CIMS, CLIPdb-CITS, and CLIPdb-Piranha-stranded datasets. We combined all the datasets for each protein within a database and divided them into three classes (Cytoplasmic, Nuclear, or Both) based on their cellular localization. The […]


Identification of high confidence RNA regulatory elements by combinatorial classification of RNA–protein binding sites

Genome Biol
PMCID: 5591525
PMID: 28886744
DOI: 10.1186/s13059-017-1298-8

[…] were also missed because our analyses did not predict new binding sites that cannot be identified from CLIP-seq data. In this paper, we used overlapped peaks defined by two computational tools (i.e. Piranha and PARalyzer); therefore, we would miss some true peaks identified by one method only. The accuracy of our results would also be significantly affected by false negatives caused by many other […]


Translation repression via modulation of the cytoplasmic poly(A) binding protein in the inflammatory response

PMCID: 5507668
PMID: 28635594
DOI: 10.7554/eLife.27786.024
call_split See protocol

[…] ads mapped to rRNA, tRNA and mitochomdrial DNA sequences using Bowtie were removed from datasets. The resulting reads were mapped to the mm10 genome by using STAR with the parameters suggested in (). Piranha () was used to call peaks from the two replicates over the input control datasets with parameters ‘-b 50 s -p 0.01’. The peaks were merged using mergePeaks function in HOMER if the distance be […]


The C Terminal SynMuv/DdDUF926 Domain Regulates the Function of the N Terminal Domain of DdNKAP

PLoS One
PMCID: 5173251
PMID: 27997579
DOI: 10.1371/journal.pone.0168617
call_split See protocol

[…] ads were aligned to the D. discoideum genome sequence (http://dictybase.org/) using Bowtie2 []. We counted reads associated with genomic features with the tophat2 program []. For peak finding we used Piranha (http://smithlabresearch.org/software/piranha/). […]


Integrating Epigenomics into the Understanding of Biomedical Insight

Bioinform Biol Insights
PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] recise cluster distribution profiles through enhancing the signal-to-noise ratio and decreasing the false-positive rate. Data analysis methods developed for this purpose include PIPE-CLIP, PARalyzer, Piranha, wavClusteR, and dCLIP. The next downstream of the pipeline is the motif discovery, higher level structure prediction, and functional characterization. Previously developed tools for DNA and p […]

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Piranha institution(s)
Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA

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