wavClusteR: Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

The package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non-experimental sources by a non- parametric mixture model. The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post-processing of the results, data export for UCSC genome browser visualization and motif search analysis are provided. In addition, the package allows to integrate RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. Note: while wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).

AuthorFederico Comoglio and Cem Sievers
Date of publicationNone
MaintainerFederico Comoglio <federico.comoglio@gmail.com>
LicenseGPL-2
Version2.8.0

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Files in this package

wavClusteR/DESCRIPTION
wavClusteR/NAMESPACE
wavClusteR/NEWS
wavClusteR/R
wavClusteR/R/FDRbyRSF.R wavClusteR/R/annotateClusters.R wavClusteR/R/export.R wavClusteR/R/filterClusters.R wavClusteR/R/fitMixtureModel.R wavClusteR/R/getAllSub.R wavClusteR/R/getClusters.R wavClusteR/R/getExpInterval.R wavClusteR/R/getHighConfSub.R wavClusteR/R/getMeta.R wavClusteR/R/plotSizeDistribution.R wavClusteR/R/plotStatistics.R wavClusteR/R/plotSubstitutions.R wavClusteR/R/processMD.R wavClusteR/R/readSortedBam.R wavClusteR/R/wavCWTPeaksCF.R wavClusteR/R/wavClusteR-package.R
wavClusteR/README.md
wavClusteR/build
wavClusteR/build/vignette.rds
wavClusteR/data
wavClusteR/data/model.rda
wavClusteR/inst
wavClusteR/inst/CITATION
wavClusteR/inst/doc
wavClusteR/inst/doc/wavCluster_vignette.R
wavClusteR/inst/doc/wavCluster_vignette.Rmd
wavClusteR/inst/doc/wavCluster_vignette.html
wavClusteR/inst/extdata
wavClusteR/inst/extdata/example.bam
wavClusteR/inst/extdata/example.bam.bai
wavClusteR/man
wavClusteR/man/FitMixtureModel.Rd wavClusteR/man/annotateClusters.Rd wavClusteR/man/estimateFDR.Rd wavClusteR/man/exportClusters.Rd wavClusteR/man/exportCoverage.Rd wavClusteR/man/exportHighConfSub.Rd wavClusteR/man/exportSequences.Rd wavClusteR/man/filterClusters.Rd wavClusteR/man/getAllSub.Rd wavClusteR/man/getClusters.Rd wavClusteR/man/getExpInterval.Rd wavClusteR/man/getHighConfSub.Rd wavClusteR/man/getMetaCoverage.Rd wavClusteR/man/getMetaGene.Rd wavClusteR/man/getMetaTSS.Rd wavClusteR/man/model.Rd wavClusteR/man/plotSizeDistribution.Rd wavClusteR/man/plotStatistics.Rd wavClusteR/man/plotSubstitutions.Rd wavClusteR/man/readSortedBam.Rd wavClusteR/man/wavClusteR-package.Rd
wavClusteR/vignettes
wavClusteR/vignettes/AGO2annotation.pdf
wavClusteR/vignettes/AGO2metagene.pdf
wavClusteR/vignettes/wavCluster_vignette.Rmd

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