Package: Damsel
Type: Package
Title: Damsel: an end to end analysis of DamID
Version: 1.4.0
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
git_url: https://git.bioconductor.org/packages/Damsel
git_branch: RELEASE_3_21
git_last_commit: 8d46949
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 00:07:25 UTC; biocbuild
Author: Caitlin Page [aut, cre] (ORCID:
    <https://orcid.org/0009-0004-7949-8143>)
Maintainer: Caitlin Page <caitlin.page@petermac.org>
Built: R 4.5.0; ; 2025-04-16 14:16:06 UTC; windows
