wavClusteR statistics

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Citations per year

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Popular tool citations

chevron_left Noise reduction Peak calling chevron_right
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Tool usage distribution map

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Associated diseases

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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


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Documentation


Maintainer


  • person_outline Federico Comoglio <>

Publications for wavClusteR

wavClusteR in publications

 (5)
PMCID: 5930818
PMID: 29716635
DOI: 10.1186/s12977-018-0417-2

[…] 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 [, […]

PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] 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 […]

PMCID: 4808798
PMID: 26751491
DOI: 10.3390/biom6010004

[…] 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. […]

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

[…] 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 […]

PMCID: 4477666
PMID: 25958398
DOI: 10.1093/nar/gkv439

[…] 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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