annotateClusters        Annotate clusters with respect to transcript
                        features
estimateFDR             Estimate False Discovery Rate within the
                        relative substitution frequency support by
                        integrating PAR-CLIP data and RNA-Seq data
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 substitutions
getAllSub               Identify all substitutions observed across
                        genomic positions exhibiting a specified
                        minimum coverage
getClusters             Identify clusters containing high-confidence
                        substitutions and resolve boundaries at high
                        resolution
getExpInterval          Identify the interval of relative substitution
                        frequencies dominated by experimental
                        induction.
getHighConfSub          Classify substitutions based on identified RSF
                        interval and return high confidence transitions
getMetaCoverage         Compute and plot distribution of average
                        coverage or relative log-odds as metagene
                        profile using identified clusters
getMetaGene             Compute and plot metagene profile using
                        identified clusters
getMetaTSS              Compute and plot read densities in genomic
                        regions around transcription start sites
model                   Components of the non-parametric mixture moodel
                        fitted on Ago2 PAR-CLIP data
plotSizeDistribution    Plot the distribution of cluster sizes
plotStatistics          Pairs plot visualization of clusters statistics
plotSubstitutions       Barplot visualization of the number of genomic
                        positions exhibiting a given substitution and,
                        if model provided, additional diagnostic plots.
readSortedBam           Load a sorted BAM file
wavClusteR-package      A comprehensive 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).
