Package: Damsel 1.3.0

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]

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Damsel.pdf |Damsel.html✨
Damsel/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:Damsel-1.1.4(bioc 3.20)Damsel-1.0.2(bioc 3.19)

differentialmethylationpeakdetectiongenepredictiongenesetenrichment

5.64 score 20 scripts 157 downloads 22 exports 172 dependencies

Last updated 23 days agofrom:7bdd2dea5c. Checks:OK: 2 ERROR: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winERROROct 30 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winERROROct 30 2024
R-4.4-macERROROct 30 2024
R-4.3-winERROROct 01 2024
R-4.3-macERROROct 01 2024

Exports:%>%annotatePeaksGenescollateGenescountBamInGATCgeom_dmgeom_gatcgeom_genes_txgeom_peakgetGatcRegionsidentifyPeaksmakeDGEplotCorrHeatmapplotCountsplotCountsDistributionplotCountsInPeaksplotGeneOntologyplotWraprandom_countsrandom_edgeR_resultsrandom_regionstestDmRegionstestGeneOntology

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiasedUrnBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIdbplyrDelayedArraydichromatdigestdoParalleldplyredgeRensembldbevaluatefansifarverfastmapfilelockfontawesomeforcatsforeachforeignformatRFormulafsfutile.loggerfutile.optionsgeneLenDataBasegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongGGallyggbioggplot2ggstatsGlobalOptionsglueGO.dbgoseqgraphgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslOrganismDbipatchworkpillarpkgconfigplogrplyrplyrangespngprettyunitsprogressProtGenericspurrrR6rappdirsRBGLRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapiRsubreadrtracklayerS4ArraysS4VectorssassscalesshapesnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc

Damsel-workflow

Rendered fromDamsel-workflow.Rmdusingknitr::rmarkdownon Oct 30 2024.

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