Package: BindingSiteFinder
Type: Package
Title: Binding site defintion based on iCLIP data
Version: 2.11.0
Authors@R: c(
    person("Mirko", "Brüggemann",
        email="mirko.brueggemann@mail.de",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0002-1778-0248")),
    person("Melina", "Klostermann",
        email="melinaklostermann@googlemail.com",
        role = c("aut"),
        comment = c(ORCID = "0000-0003-3122-1095")),
    person("Kathi", "Zarnack",
        email="kathi.zarnack@bmls.de",
        role = c("aut"),
        comment = c(ORCID = "0000-0003-3527-3378")))
Description: Precise knowledge on the binding sites of an RNA-binding
        protein (RBP) is key to understand (post-) transcriptional
        regulatory processes. Here we present a workflow that describes
        how exact binding sites can be defined from iCLIP data. The
        package provides functions for binding site definition and
        result visualization. For details please see the vignette.
License: Artistic-2.0
Encoding: UTF-8
VignetteBuilder: knitr
Imports: tidyr, tibble, plyr, matrixStats, stats, ggplot2, methods,
        rtracklayer, S4Vectors, ggforce, GenomeInfoDb, ComplexHeatmap,
        RColorBrewer, lifecycle, rlang, forcats, dplyr,
        GenomicFeatures, IRanges, kableExtra, ggdist
Depends: GenomicRanges, R (>= 4.2)
Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments,
        scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify,
        SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr,
        txdbmaker, ggrepel, stringr
RoxygenNote: 7.3.2
Collate: 'AllClasses.R' 'AllGenerics.R' 'Functions.R' 'methods.R'
        'bindingsites.R' 'helper.R' 'PlotFunction.R'
        'CoverageFunctions.R' 'workflow.R' 'helperSpecific.R'
        'exports.R' 'coveragePlots.R' 'bsfind.R' 'helperPlots.R'
        'differentialFunctions.R' 'differentialPlots.R'
biocViews: Sequencing, GeneExpression, GeneRegulation,
        FunctionalGenomics, Coverage, DataImport
BugReports: https://github.com/ZarnackGroup/BindingSiteFinder/issues
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev make libharfbuzz-dev libbz2-dev libicu-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev perl
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:56:33 UTC
RemoteUrl: https://github.com/bioc/BindingSiteFinder
RemoteRef: HEAD
RemoteSha: aec001f676114d29c45d7ffb6599cd6f075973a6
NeedsCompilation: no
Packaged: 2026-07-03 14:54:20 UTC; root
Author: Mirko Brüggemann [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1778-0248>),
  Melina Klostermann [aut] (ORCID:
    <https://orcid.org/0000-0003-3122-1095>),
  Kathi Zarnack [aut] (ORCID: <https://orcid.org/0000-0003-3527-3378>)
Maintainer: Mirko Brüggemann <mirko.brueggemann@mail.de>