Package: Damsel 1.9.0

Caitlin Page

Damsel: Damsel: an end to end analysis of DamID

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.

Authors:Caitlin Page [aut, cre]

Damsel_1.9.0.tar.gz
Damsel_1.9.0.zip(r-4.7)Damsel_1.9.0.zip(r-4.6)Damsel_1.9.0.zip(r-4.5)
Damsel_1.9.0.tgz(r-4.6-any)Damsel_1.9.0.tgz(r-4.5-any)
Damsel_1.9.0.tar.gz(r-4.7-any)Damsel_1.9.0.tar.gz(r-4.6-any)
Damsel_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Damsel/json (API)
NEWS

# Install 'Damsel' in R:
install.packages('Damsel', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/oshlack/damsel/issues

Datasets:

On BioConductor:Damsel-1.9.0(bioc 3.24)Damsel-1.8.0(bioc 3.23)

differentialmethylationpeakdetectiongenepredictiongenesetenrichment

4.62 score 1 stars 21 scripts 292 downloads 22 exports 166 dependencies

Last updated from:08681dc371. Checks:1 NOTE, 4 ERROR, 2 OK, 3 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE294
linux-devel-x86_64ERROR528
source / vignettesOK599
linux-release-x86_64WARNING520
macos-release-arm64ERROR1013
macos-oldrel-arm64ERROR762
windows-develERROR525
windows-releaseWARNING436
windows-oldrelWARNING347
wasm-releaseOK290

Exports:%>%annotatePeaksGenescollateGenescountBamInGATCgeom_dmgeom_gatcgeom_genes_txgeom_peakgetGatcRegionsidentifyPeaksmakeDGEplotCorrHeatmapplotCountsplotCountsDistributionplotCountsInPeaksplotGeneOntologyplotWraprandom_countsrandom_edgeR_resultsrandom_regionstestDmRegionstestGeneOntology

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiasedUrnBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIdbplyrDelayedArraydichromatdigestdoParalleldplyredgeRensembldbevaluatefarverfastmapfilelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgeneLenDataBasegenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggbioggplot2GlobalOptionsglueGO.dbgoseqgraphgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmennetopensslOrganismDbipatchworkpillarpkgconfigplyrplyrangespngprettyunitsprogressProtGenericspurrrR6rappdirsRBGLRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapiRsubreadrtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoshapesnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml

Damsel-workflow

Rendered fromDamsel-workflow.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2024-10-01
Started: 2024-03-04