wavClusteR statistics

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Citations per year

Number of citations per year for the bioinformatics software tool wavClusteR

Tool usage distribution map

This map represents all the scientific publications referring to wavClusteR per scientific context
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Associated diseases


Popular tool citations

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wavClusteR specifications


Unique identifier OMICS_02255
Name wavClusteR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 2.1.0
Stability Stable
GenomicRanges, Rsamtools
Maintained Yes


No version available



  • person_outline Federico Comoglio

Publications for wavClusteR

wavClusteR citations


CLIP related methodologies and their application to retrovirology

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

[…] etween 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 statistical models underlying these programs, we refer the readers to detailed reviews on this topic [, ].Post […]


Integrating Epigenomics into the Understanding of Biomedical Insight

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

[…] uster 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 protein mo […]


Guardian of Genetic Messenger RNA Binding Proteins

PMCID: 4808798
PMID: 26751491
DOI: 10.3390/biom6010004

[…] ads with a length above a certain threshold are considered for further analysis to detect RBP binding sites. RBP binding site detection is a challenging process. Several computational methods such as WavClusteR, PARalyzer, Piranha, PIPE-CLIP, dCLIP, and GraphProt have been developed and utilized to detect RBP binding sites while minimizing the detection of false positives and background. Computati […]


Revealing protein–lncRNA interaction

Brief Bioinform
PMCID: 4719072
PMID: 26041786
DOI: 10.1093/bib/bbv031

[…] sence of a sufficient number of CIMS or PAR-CLIP transitions in each cluster reduced the number of false hits. A number of sophisticated algorithms have been developed, e.g. PARalyzer [], Piranha [], wavClusteR [], RIPSeeker [], MiClip [], PIPE-CLIP [] and the Pyicoclip module of the Pyicoteo toolkit (previously called Pyicos) []. While different in implementation, all these procedures can be summ […]


Design and bioinformatics analysis of genome wide CLIP experiments

Nucleic Acids Res
PMCID: 4477666
PMID: 25958398
DOI: 10.1093/nar/gkv439

[…] inking sites. Low mutant tag ratios in some experiments could be problematic for bioinformatics pipelines for analyzing HITS-CLIP and PAR-CLIP data that utilize mutation ratios, such as MiClip () and wavClusteR (). On the other hand, there may be a small number of bases covered by CLIP clusters that show close to 100% mutant rates, which are likely SNPs in the cell lines or tissue samples instead […]

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wavClusteR institution(s)
Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zurich, Basel, Switzerland

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