Package: wavClusteR
Type: Package
Title: Sensitive and highly resolved identification of RNA-protein interaction
    sites in PAR-CLIP data
Version: 2.45.0
Date: 2015-05-07
Depends:
    R (>= 3.2),
    GenomicRanges (>= 1.31.8),
    Rsamtools
Imports:
    methods,
    BiocGenerics,
    S4Vectors (>= 0.17.25),
    IRanges (>= 2.13.12),
    Biostrings (>= 2.47.6),
    foreach,
    GenomicFeatures (>= 1.31.3),
    ggplot2,
    Hmisc,
    mclust,
    rtracklayer (>= 1.39.7),
    seqinr,
    stringr
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: ImmunoOncology, Sequencing, Technology, RIPSeq, RNASeq, Bayesian
LazyLoad: yes
RoxygenNote: 7.0.2
git_url: https://git.bioconductor.org/packages/wavClusteR
git_branch: devel
git_last_commit: f078fce
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
