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
git_url: https://git.bioconductor.org/packages/damidBind
git_branch: RELEASE_3_23
git_last_commit: 0b48cef
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
NeedsCompilation: no
Packaged: 2026-04-28 21:53:19 UTC; biocbuild
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 04:39:26 UTC; unix
