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Damsel: an end to end analysis of DamID

Bioconductor version: Release (3.19)

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.

Author: Caitlin Page [aut, cre]

Maintainer: Caitlin Page < at>

Citation (from within R, enter citation("Damsel")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Damsel-workflow HTML R Script
Reference Manual PDF


biocViews DifferentialMethylation, GenePrediction, GeneSetEnrichment, PeakDetection, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.4.0)
Imports AnnotationDbi, Biostrings, dplyr, edgeR, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggbio, ggplot2, goseq, magrittr, patchwork, plyranges, reshape2, rlang, Rsamtools, Rsubread, stats, stringr, tidyr, utils
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Suggests BiocStyle, biomaRt, biovizBase, BSgenome.Dmelanogaster.UCSC.dm6, knitr, limma,, rmarkdown, testthat (>= 3.0.0), TxDb.Dmelanogaster.UCSC.dm6.ensGene
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Follow Installation instructions to use this package in your R session.

Source Package Damsel_1.0.0.tar.gz
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macOS Binary (x86_64) Damsel_1.0.0.tgz
macOS Binary (arm64) Damsel_1.0.0.tgz
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Source Repository (Developer Access) git clone
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