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]

tidyCoverage_1.9.0.tar.gz
tidyCoverage_1.9.0.zip(r-4.7)tidyCoverage_1.9.0.zip(r-4.6)tidyCoverage_1.9.0.zip(r-4.5)
tidyCoverage_1.9.0.tgz(r-4.6-any)tidyCoverage_1.9.0.tgz(r-4.5-any)
tidyCoverage_1.9.0.tar.gz(r-4.7-any)tidyCoverage_1.9.0.tar.gz(r-4.6-any)
tidyCoverage_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
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

5.78 score 24 stars 10 scripts 258 downloads 8 exports 88 dependencies

Last updated from:c3c722da2b. Checks:1 WARNING, 4 NOTE, 2 OK, 3 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING225
linux-devel-x86_64NOTE497
source / vignettesOK431
linux-release-x86_64NOTE514
macos-release-arm64NOTE219
macos-oldrel-arm64NOTE257
windows-develERROR356
windows-releaseERROR331
windows-oldrelERROR333
wasm-releaseOK203

Exports:aggregatecoarsenCoverageExperimentgeom_aggrcoveragegeom_coveragescale_x_genomescale_y_coverageshow

Dependencies:abindaskpassbase64encbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsCairocigarilloclicodetoolscpp11crayoncurlDelayedArraydplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggbeeswarmggplot2ggrastrgluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpngpurrrR6raggRColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselectUCSC.utilsutf8vctrsviporviridisLitewithrXMLXVectoryaml

Introduction to tidyCoverage

Rendered fromtidyCoverage.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2025-12-20
Started: 2023-11-27

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