Package: wavClusteR
Type: Package
Title: wavClusteR
Version: 2.0.0
Date: 2014-03-08
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
Author: Federico Comoglio and Cem Sievers
Maintainer: Federico Comoglio <federico.comoglio@bsse.ethz.ch>
Description: 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)
License: GPL-2
biocViews: Sequencing, Software
LazyLoad: yes
Packaged: 2014-10-14 05:06:52 UTC; biocbuild
Built: R 3.1.1; ; 2014-10-14 14:19:33 UTC; windows
