Package: wavClusteR
Type: Package
Title: Sensitive and highly resolved identification of RNA-protein
        interaction sites in PAR-CLIP data
Version: 2.12.1
Date: 2018-04-05
Depends: R (>= 3.2), GenomicRanges (>= 1.23.16), Rsamtools
Imports: methods, BiocGenerics, S4Vectors (>= 0.9.25), IRanges (>=
        2.5.27), Biostrings, foreach, GenomicFeatures, ggplot2, Hmisc,
        mclust, rtracklayer, seqinr, stringr, wmtsa
Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19
Enhances: doMC
VignetteBuilder: knitr
Author: Federico Comoglio and Cem Sievers
Maintainer: Federico Comoglio <federico.comoglio@gmail.com>
Description: 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).
License: GPL-2
biocViews: Sequencing, Technology, RIPSeq, RNASeq, Bayesian
LazyLoad: yes
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2018-04-06 00:32:34 UTC; biocbuild
Built: R 3.4.4; ; 2018-04-06 08:03:40 UTC; windows
