Package: Damsel 1.1.0
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:
Damsel_1.1.0.tar.gz
Damsel_1.1.0.zip(r-4.5)Damsel_1.1.0.zip(r-4.4)Damsel_1.1.0.zip(r-4.3)
Damsel_1.1.0.tgz(r-4.4-any)Damsel_1.1.0.tgz(r-4.3-any)
Damsel_1.1.0.tar.gz(r-4.5-noble)Damsel_1.1.0.tar.gz(r-4.4-noble)
Damsel_1.1.0.tgz(r-4.4-emscripten)Damsel_1.1.0.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/oshlack/damsel/issues
- dros_counts - Example Drosophila DamID counts
On BioConductor:Damsel-1.1.0(bioc 3.20)Damsel-1.0.0(bioc 3.19)
Last updated 2 months agofrom:1d9779e30d
Exports:%>%annotatePeaksGenescollateGenescountBamInGATCgeom_dmgeom_gatcgeom_genes_txgeom_peakgetGatcRegionsidentifyPeaksmakeDGEplotCorrHeatmapplotCountsplotGeneOntologyplotWraprandom_countsrandom_edgeR_resultsrandom_regionstestDmRegionstestGeneOntology
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiasedUrnBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobbroombroom.helpersBSgenomebslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydichromatdigestdplyredgeRensembldbevaluatefansifarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgeneLenDataBasegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGGallyggbioggplot2ggstatsglueGO.dbgoseqgraphgridExtragtablehavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglabelledlambda.rlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslOrganismDbipatchworkpillarpkgconfigplogrplyrplyrangespngprettyunitsprogressProtGenericspurrrR6rappdirsRBGLRColorBrewerRcppRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapiRsubreadrtracklayerS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakertzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotation of peaks and genes | annotatePeaksGenes |
| Get list of genes | collateGenes |
| Obtain region counts for BAM files | countBamInGATC |
| Example Drosophila DamID counts | dros_counts |
| Plotting results from differential methylation testing | geom_dm |
| Plot for a GATC track | geom_gatc |
| Plotting genes | geom_genes_tx |
| Plotting peaks | geom_peak |
| Extract GATC regions | getGatcRegions |
| Identify peaks from differentially methylated regions | identifyPeaks |
| Create DGE object for differential testing | makeDGE |
| Plot correlation heatmap | plotCorrHeatmap |
| Plot for counts for all samples across a given region | plotCounts |
| Plot gene ontology results | plotGeneOntology |
| Wrapper function for plotting | plotWrap |
| Create example counts | random_counts |
| Create example edgeR results | random_edgeR_results |
| Create example regions | random_regions |
| Differential testing | testDmRegions |
| Gene ontology analysis | testGeneOntology |