wavClusteR statistics

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Citations per year

Number of citations per year for the bioinformatics software tool wavClusteR
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Tool usage distribution map

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

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Popular tool citations

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wavClusteR specifications

Information


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
Requirements
GenomicRanges, Rsamtools
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Federico Comoglio

Publications for wavClusteR

wavClusteR citations

 (5)
library_books

CLIP related methodologies and their application to retrovirology

2018
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 […]

library_books

Integrating Epigenomics into the Understanding of Biomedical Insight

2016
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 […]

library_books

Guardian of Genetic Messenger RNA Binding Proteins

2016
Biomolecules
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 […]

library_books

Revealing protein–lncRNA interaction

2015
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 […]

library_books

Design and bioinformatics analysis of genome wide CLIP experiments

2015
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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