Introduction | Installation | CoverageExperiment and AggregatedCoverage classes | CoverageExperiment | AggregatedCoverage | Manipulate CoverageExperiment objects | Create a CoverageExperiment object | Bin a CoverageExperiment object | Expand a CoverageExperiment object | Plot coverage of a set of tracks over a single genomic locus | Manipulate AggregatedCoverage objects | Aggregate a CoverageExperiment into an AggregatedCoverage object | AggregatedCoverage over multiple tracks / feature sets | Plot aggregated coverages with ggplot2 | Use a tidy grammar | Example workflow using tidy grammar | Example use case: AnnotationHub and TxDb resources | Recover TSSs of forward mouse genes | Recover H3K4me3 coverage track from AnnotationHub | Compute the aggregated coverage of H3K4me3 ± 3kb around the TSSs of forward mouse genes | With more genomic tracks | Session info
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:
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✨
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:
On BioConductor:tidyCoverage-1.9.0(bioc 3.24)tidyCoverage-1.8.0(bioc 3.23)
Last updated from:c3c722da2b. Checks:1 WARNING, 4 NOTE, 2 OK, 3 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 260 | ||
| linux-devel-x86_64 | NOTE | 539 | ||
| source / vignettes | OK | 448 | ||
| linux-release-x86_64 | NOTE | 486 | ||
| macos-release-arm64 | NOTE | 349 | ||
| macos-oldrel-arm64 | NOTE | 314 | ||
| windows-devel | ERROR | 340 | ||
| windows-release | ERROR | 323 | ||
| windows-oldrel | ERROR | 340 | ||
| wasm-release | OK | 220 |
Exports:aggregatecoarsenCoverageExperimentgeom_aggrcoveragegeom_coveragescale_x_genomescale_y_coverageshow
Dependencies:abindaskpassbase64encbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsCairocigarilloclicodetoolscpp11crayoncurlDelayedArraydplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggbeeswarmggplot2ggrastrgluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpngpurrrR6raggRColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselectUCSC.utilsutf8vctrsviporviridisLitewithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| aggregate | aggregate,CoverageExperiment-method AggregatedCoverage |
| as_tibble | as_tibble-AggregatedCoverage as_tibble.AggregatedCoverage |
| CoverageExperiment | coarsen 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' objects | ac ce data |
| Expand a CoverageExperiment object | expand-CoverageExperiment expand.CoverageExperiment |
| Plotting functions | geom_aggrcoverage geom_coverage ggplot-tidyCoverage scale_x_genome scale_y_coverage |
| show method for 'CoverageExperiment' and 'AggregatedCoverage' objects | show,AggregatedCoverage-method show,CoverageExperiment-method show-tidyCoverage |
