Package: tidyCoverage 1.9.0

Jacques Serizay

tidyCoverage: Extract and aggregate genomic coverage over features of interest

`tidyCoverage` framework enables tidy manipulation of collections of genomic tracks and features using `tidySummarizedExperiment` methods. It facilitates the extraction, aggregation and visualization of genomic coverage over individual or thousands of genomic loci, relying on `CoverageExperiment` and `AggregatedCoverage` classes. This accelerates the integration of genomic track data in genomic analysis workflows.

Authors:Jacques Serizay [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
tidyCoverage/json (API)

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

Bug tracker:https://github.com/js2264/tidycoverage/issues

Datasets:
  • ac - Example 'CoverageExperiment' and 'AggregatedCoverage' objects
  • ce - Example 'CoverageExperiment' and 'AggregatedCoverage' objects

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

softwaresequencingcoverage

4.80 score 25 stars 10 scripts 363 downloads 8 exports 88 dependencies

Last updated from:c3c722da2b. Checks:5 WARNING, 4 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING206
linux-develWARNING527
source / vignettesERROR384
linux-releaseWARNING411
macos-releaseWARNING226
macos-oldrelWARNING310
windows-develERROR318
windows-releaseERROR317
windows-oldrelERROR299
wasm-releaseOK166

Exports:aggregatecoarsenCoverageExperimentgeom_aggrcoveragegeom_coveragescale_x_genomescale_y_coverageshow

Dependencies:abindaskpassbase64encbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsCairocigarilloclicodetoolscpp11crayoncurlDelayedArraydplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggbeeswarmggplot2ggrastrgluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpngpurrrR6raggRColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselectUCSC.utilsutf8vctrsviporviridisLitewithrXMLXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
aggregateaggregate,CoverageExperiment-method AggregatedCoverage
as_tibbleas_tibble-AggregatedCoverage as_tibble.AggregatedCoverage
CoverageExperimentcoarsen coarsen,CoverageExperiment-method CoverageExperiment CoverageExperiment,BigWigFile,GRanges-method CoverageExperiment,BigWigFile,GRangesList-method CoverageExperiment,BigWigFile,list-method CoverageExperiment,BigWigFileList,GRanges-method CoverageExperiment,BigWigFileList,GRangesList-method CoverageExperiment,BigWigFileList,list-method CoverageExperiment,list,GRanges-method CoverageExperiment,list,GRangesList-method CoverageExperiment,list,list-method CoverageExperiment,RleList,GRanges-method CoverageExperiment,RleList,GRangesList-method CoverageExperiment,RleList,list-method
Example 'CoverageExperiment' and 'AggregatedCoverage' objectsac ce data
Expand a CoverageExperiment objectexpand-CoverageExperiment expand.CoverageExperiment
Plotting functionsgeom_aggrcoverage geom_coverage ggplot-tidyCoverage scale_x_genome scale_y_coverage
show method for 'CoverageExperiment' and 'AggregatedCoverage' objectsshow,AggregatedCoverage-method show,CoverageExperiment-method show-tidyCoverage