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Bioconductor version: 3.0

Infer PAR-CLIP induced transitions and discriminate them from sequencing error, SNPs, contaminants and additional non-experimental causes, using a non-parametric mixture model. wavClusteR resolves cluster boundaries at high resolution and provides robust estimation of cluster statistics. In addition, the package allows to integrate RNA-Seq data to estimate FDR over the entire range of relative substitution frequencies. Furthermore, the package provides post-processing of results and functions to export results for UCSC genome browser visualization and motif search analysis. Key functions support parallel multicore computing. While wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other Next-Generation Sequencing data obtained from substitution inducing experimental procedures (e.g. BisSeq)

Author: Federico Comoglio and Cem Sievers

Maintainer: Federico Comoglio <federico.comoglio at>

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PDF R Script wavClusteR
PDF   Reference Manual


biocViews Sequencing, Software
Version 2.0.0
In Bioconductor since BioC 3.0 (R-3.1)
License GPL-2
Depends R (>= 3.0.0), GenomicRanges, Rsamtools
Imports Biostrings, foreach, GenomicFeatures, ggplot2, Hmisc, IRanges, mclust, rtracklayer, seqinr, stringr, wmtsa
Suggests BSgenome.Hsapiens.UCSC.hg19
Enhances doMC
Depends On Me
Imports Me
Suggests Me
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