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

View on Bioconductor

Functions

annotateClusters Man page
estimateFDR Man page
exportClusters Man page
exportCoverage Man page
exportHighConfSub Man page
exportSequences Man page
filterClusters Man page
fitMixtureModel Man page
getAllSub Man page
getClusters Man page
getExpInterval Man page
getHighConfSub Man page
getMetaCoverage Man page
getMetaGene Man page
getMetaTSS Man page
model Man page
plotSizeDistribution Man page
plotStatistics Man page
plotSubstitutions Man page
readSortedBam Man page
wavClusteR Man page
wavClusteR-package Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.