Package: wavClusteR
Type: Package
Title: Sensitive and highly resolved identification of RNA-protein
        interaction sites in PAR-CLIP data
Version: 2.47.0
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, txdbmaker
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
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:39:13 UTC
RemoteUrl: https://github.com/bioc/wavClusteR
RemoteRef: HEAD
RemoteSha: 231077608f4a1af7146a4b1c1f29e692fe93d5d8
NeedsCompilation: no
Packaged: 2026-07-03 06:26:19 UTC; root