Package: BindingSiteFinder
Type: Package
Title: Binding site defintion based on iCLIP data
Version: 2.9.0
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: libfontconfig1-dev libfreetype6-dev libfribidi-dev
        make libharfbuzz-dev libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev perl xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:10:55 UTC
RemoteUrl: https://github.com/bioc/BindingSiteFinder
RemoteRef: HEAD
RemoteSha: 885c4f6e7b42738891b9d13cdf7c0110cac24148
NeedsCompilation: no
Packaged: 2026-01-09 21:09:50 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>
Built: R 4.6.0; ; 2026-01-09 21:13:44 UTC; windows
