Package: damidBind
Type: Package
Title: Differential Binding and Expression Analysis for DamID-seq Data
Version: 1.0.0
Authors@R: 
    person("Owen", "Marshall", 
    email = "owen.marshall@utas.edu.au", 
    role = c("aut", "cre"), 
    comment = c(ORCID = "0000-0003-1605-3871"))
Description: The damidBind package provides a straightforward formal
        analysis pipeline to analyse and explore differential DamID
        binding, gene transcription or chromatin accessibility between
        two conditions. The package imports processed data from
        DamID-seq experiments, either as external raw files in the form
        of binding bedGraphs and GFF/BED peak calls, or as internal
        lists of GRanges objects. After optionally normalising data,
        combining peaks across replicates and determining per-replicate
        peak occupancy, the package links bound loci to nearby genes.
        For RNA Polymerase DamID data, the package calculates occupancy
        over genes, and optionally calcualates the FDR of
        significantly-enriched gene occupancy. damidBind then uses
        either limma (for conventional log2 ratio DamID binding data)
        or NOIseq (for counts-based CATaDa chromatin accessibility
        data) to identify differentially-enriched regions, or
        differentially epxressed genes, between two conditions. The
        package provides a number of visualisation tools (volcano
        plots, Gene Ontology enrichment plots via ClusterProfiler and
        proportional Venn diagrams via BioVenn for downstream data
        exploration and analysis. An powerful, interactive IGV genome
        browser interface (powered by Shiny and igvShiny) allows users
        to rapidly and intuitively assess significant
        differentially-bound regions in their genomic context.
License: GPL-3
Encoding: UTF-8
biocViews: DifferentialExpression, GeneExpression, Transcription,
        Epigenetics, Visualization, Sequencing, Software,
        GeneRegulation
Depends: R (>= 4.4.0)
Imports: ggplot2, ggrepel, dplyr, tibble, stringr, tools, fs, rlang,
        BiocParallel, AnnotationHub, DBI, ensembldb, GenomeInfoDb,
        IRanges, GenomicRanges, S4Vectors, rtracklayer, limma, NOISeq,
        BioVenn, clusterProfiler, enrichplot, forcats, scales,
        colorspace, ggnewscale, methods, stats, igvShiny, shiny, DT,
        dbscan, circlize, ComplexHeatmap, patchwork, splines
Suggests: testthat, curl, knitr, htmltools, rmarkdown, BiocStyle,
        bookdown, org.Dm.eg.db
RoxygenNote: 7.3.3
VignetteBuilder: knitr
URL: https://marshall-lab.org/damidBind
BugReports: https://github.com/marshall-lab/damidBind/issues
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make
        libharfbuzz-dev libbz2-dev libicu-dev liblzma-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev perl libnode-dev xz-utils
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:06:03 UTC
RemoteUrl: https://github.com/bioc/damidBind
RemoteRef: RELEASE_3_23
RemoteSha: 0b48cef2ab7b685b4e573703594e2c6a55c16511
NeedsCompilation: no
Packaged: 2026-04-29 20:59:50 UTC; root
Author: Owen Marshall [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1605-3871>)
Maintainer: Owen Marshall <owen.marshall@utas.edu.au>
Built: R 4.6.0; ; 2026-04-29 21:06:14 UTC; windows
