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

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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).

Author
Federico Comoglio and Cem Sievers
Date of publication
None
Maintainer
Federico Comoglio <federico.comoglio@gmail.com>
License
GPL-2
Version
2.8.0

View on Bioconductor

Man pages

annotateClusters
Annotate clusters with respect to transcript features
estimateFDR
Estimate False Discovery Rate within the relative...
exportClusters
Export clusters as BED track
exportCoverage
Export coverage as BigWig track
exportHighConfSub
Export high-confidence substitutions as BED track
exportSequences
Export cluster sequences for motif search analysis
filterClusters
Merge clusters and compute all relevant cluster statistics
FitMixtureModel
Fit a non-parametric mixture model from all identified...
getAllSub
Identify all substitutions observed across genomic positions...
getClusters
Identify clusters containing high-confidence substitutions...
getExpInterval
Identify the interval of relative substitution frequencies...
getHighConfSub
Classify substitutions based on identified RSF interval and...
getMetaCoverage
Compute and plot distribution of average coverage or relative...
getMetaGene
Compute and plot metagene profile using identified clusters
getMetaTSS
Compute and plot read densities in genomic regions around...
model
Components of the non-parametric mixture moodel fitted on...
plotSizeDistribution
Plot the distribution of cluster sizes
plotStatistics
Pairs plot visualization of clusters statistics
plotSubstitutions
Barplot visualization of the number of genomic positions...
readSortedBam
Load a sorted BAM file
wavClusteR-package
A comprehensive pipeline for the analysis of PAR-CLIP data....

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