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

# 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:

dros_counts - Example Drosophila DamID counts

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

differentialmethylation peakdetection geneprediction genesetenrichment

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.

Target	Result	Time
bioc-checks	NOTE	294
linux-devel-x86_64	ERROR	528
source / vignettes	OK	599
linux-release-x86_64	WARNING	520
macos-release-arm64	ERROR	1013
macos-oldrel-arm64	ERROR	762
windows-devel	ERROR	525
windows-release	WARNING	436
windows-oldrel	WARNING	347
wasm-release	OK	290

Exports:%>%annotatePeaksGenes collateGenes countBamInGATC geom_dm geom_gatc geom_genes_tx geom_peak getGatcRegions identifyPeaks makeDGE plotCorrHeatmap plotCounts plotCountsDistribution plotCountsInPeaks plotGeneOntology plotWrap random_counts random_edgeR_results random_regions testDmRegions testGeneOntology

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH BiasedUrn Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl data.table DBI dbplyr DelayedArray dichromat digest doParallel dplyr edgeR ensembldb evaluate farver fastmap filelock fontawesome foreach foreign formatR Formula fs futile.logger futile.options geneLenDataBase generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggbio ggplot2 GlobalOptions glue GO.db goseq graph gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mgcv mime nlme nnet openssl OrganismDbi patchwork pillar pkgconfig plyr plyranges png prettyunits progress ProtGenerics purrr R6 rappdirs RBGL RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi Rsubread rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo shape snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr xfun XML xml2 XVector yaml

Damsel-workflow

Rendered fromDamsel-workflow.Rmdusingknitr::rmarkdown

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

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 distribution of counts `plotCountsDistribution` plots the distribution of counts enabling the comparison of different samples. Can highlight the different library sizes of the samples.	plotCountsDistribution
Plotting the	plotCountsInPeaks
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

Package: Damsel 1.9.0

Damsel: Damsel: an end to end analysis of DamID

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