wavClusteR: Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
Version 2.10.0

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
Bioconductor views Bayesian RIPSeq RNASeq Sequencing Technology
Date of publicationNone
MaintainerFederico Comoglio <federico.comoglio@gmail.com>
LicenseGPL-2
Version2.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("wavClusteR")

Getting started

Package overview
README.md
wavClusteR: a workflow for PAR-CLIP data analysis

Popular man pages

estimateFDR: Estimate False Discovery Rate within the relative...
exportSequences: Export cluster sequences for motif search analysis
getMetaGene: Compute and plot metagene profile using identified clusters
getMetaTSS: Compute and plot read densities in genomic regions around...
plotSizeDistribution: Plot the distribution of cluster sizes
readSortedBam: Load a sorted BAM file
wavClusteR-package: A comprehensive pipeline for the analysis of PAR-CLIP data....
See all...

All man pages Function index File listing

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....

Functions

annotateClusters Man page Source code
computeLogOdds Source code
computePosterior Source code
computelogOdds Source code
estimateFDR Man page Source code
estimateP Source code
exportClusters Man page Source code
exportCoverage Man page Source code
exportGR Source code
exportHighConfSub Man page Source code
exportSequences Man page Source code
filterClusters Man page Source code
filterClustersCWT Source code
filterClustersMRN Source code
fitMixtureModel Man page Source code
getAllSub Man page Source code
getClusters Man page Source code
getClustersCWT Source code
getClustersMRN Source code
getComplSubst Source code
getCountTable Source code
getCoverageAtSubst Source code
getExpInterval Man page Source code
getHighConfSub Man page Source code
getLogOdd Source code
getMetaCoverage Man page Source code
getMetaGene Man page Source code
getMetaTSS Man page Source code
getOdd Source code
getSEcoverage Source code
getSignal Source code
getWindow Source code
learnThreshold Source code
leftBound Source code
model Man page
plotSizeDistribution Man page Source code
plotStatistics Man page Source code
plotSubstitutions Man page Source code
processChunk Source code
processMD Source code
readSortedBam Man page Source code
rightBound Source code
wavCWTPeaksCF Source code
wavClusteR Man page
wavClusteR-package Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/FDRbyRSF.R
R/annotateClusters.R
R/export.R
R/filterClusters.R
R/fitMixtureModel.R
R/getAllSub.R
R/getClusters.R
R/getExpInterval.R
R/getHighConfSub.R
R/getMeta.R
R/plotSizeDistribution.R
R/plotStatistics.R
R/plotSubstitutions.R
R/processMD.R
R/readSortedBam.R
R/wavCWTPeaksCF.R
R/wavClusteR-package.R
README.md
build
build/vignette.rds
data
data/model.rda
inst
inst/CITATION
inst/doc
inst/doc/wavCluster_vignette.R
inst/doc/wavCluster_vignette.Rmd
inst/doc/wavCluster_vignette.html
inst/extdata
inst/extdata/example.bam
inst/extdata/example.bam.bai
man
man/FitMixtureModel.Rd
man/annotateClusters.Rd
man/estimateFDR.Rd
man/exportClusters.Rd
man/exportCoverage.Rd
man/exportHighConfSub.Rd
man/exportSequences.Rd
man/filterClusters.Rd
man/getAllSub.Rd
man/getClusters.Rd
man/getExpInterval.Rd
man/getHighConfSub.Rd
man/getMetaCoverage.Rd
man/getMetaGene.Rd
man/getMetaTSS.Rd
man/model.Rd
man/plotSizeDistribution.Rd
man/plotStatistics.Rd
man/plotSubstitutions.Rd
man/readSortedBam.Rd
man/wavClusteR-package.Rd
vignettes
vignettes/AGO2annotation.pdf
vignettes/AGO2metagene.pdf
vignettes/wavCluster_vignette.Rmd
wavClusteR documentation built on May 20, 2017, 9:14 p.m.

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