Package: Damsel
Type: Package
Title: Damsel: an end to end analysis of DamID
Version: 1.6.0
Authors@R: person("Caitlin", "Page", 
    email = "caitlin.page@petermac.org", role = c("aut", "cre"),
    comment = c(ORCID = "0009-0004-7949-8143"))
Description: Damsel provides an end to end analysis of DamID data.
        Damsel takes bam files from Dam-only control and fusion samples
        and counts the reads matching to each GATC region. edgeR is
        utilised to identify regions of enrichment in the fusion
        relative to the control. Enriched regions are combined into
        peaks, and are associated with nearby genes. Damsel allows for
        IGV style plots to be built as the results build, inspired by
        ggcoverage, and using the functionality and layering ability of
        ggplot2. Damsel also conducts gene ontology testing with bias
        correction through goseq, and future versions of Damsel will
        also incorporate motif enrichment analysis. Overall, Damsel is
        the first package allowing for an end to end analysis with
        visual capabilities. The goal of Damsel was to bring all the
        analysis into one place, and allow for exploratory analysis
        within R.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: BiocStyle, biomaRt, biovizBase,
        BSgenome.Dmelanogaster.UCSC.dm6, knitr, limma, org.Dm.eg.db,
        rmarkdown, testthat (>= 3.0.0),
        TxDb.Dmelanogaster.UCSC.dm6.ensGene
Config/testthat/edition: 3
Depends: R (>= 4.4.0)
RoxygenNote: 7.3.1
Imports: AnnotationDbi, Biostrings, ComplexHeatmap, dplyr, edgeR,
        GenomeInfoDb, GenomicFeatures, GenomicRanges, ggbio, ggplot2,
        goseq, magrittr, patchwork, plyranges, reshape2, rlang,
        Rsamtools, Rsubread, stats, stringr, tidyr, utils
BugReports: https://github.com/Oshlack/Damsel
URL: https://github.com/Oshlack/Damsel
biocViews: DifferentialMethylation, PeakDetection, GenePrediction,
        GeneSetEnrichment
VignetteBuilder: knitr
LazyData: FALSE
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev perl
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:29:38 UTC
RemoteUrl: https://github.com/bioc/Damsel
RemoteRef: RELEASE_3_22
RemoteSha: a70f6d8a8b445722396ecd7d550c1b62591ca8f5
NeedsCompilation: no
Packaged: 2025-11-11 16:49:36 UTC; root
Author: Caitlin Page [aut, cre] (ORCID:
    <https://orcid.org/0009-0004-7949-8143>)
Maintainer: Caitlin Page <caitlin.page@petermac.org>
Built: R 4.5.2; ; 2025-11-11 17:00:18 UTC; windows
