Package: wavClusteR
Type: Package
Title: Sensitive and highly resolved identification of RNA-protein
        interaction sites in PAR-CLIP data
Version: 2.2.0
Date: 2015-13-02
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: 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).
License: GPL-2
biocViews: HighThroughputSequencing, Software
LazyLoad: yes
NeedsCompilation: no
Packaged: 2015-04-17 05:16:08 UTC; biocbuild
Built: R 3.2.0; ; 2015-04-17 14:09:06 UTC; windows
