Package: CopyNumberPlots 1.23.0

Bernat Gel

CopyNumberPlots: Create Copy-Number Plots using karyoploteR functionality

CopyNumberPlots have a set of functions extending karyoploteRs functionality to create beautiful, customizable and flexible plots of copy-number related data.

Authors:Bernat Gel <[email protected]> and Miriam Magallon <[email protected]>

CopyNumberPlots_1.23.0.tar.gz
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CopyNumberPlots.pdf |CopyNumberPlots.html✨
CopyNumberPlots/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/bernatgel/copynumberplots/issues

On BioConductor:CopyNumberPlots-1.21.0(bioc 3.20)CopyNumberPlots-1.20.0(bioc 3.19)

visualizationcopynumbervariationcoverageonechanneldataimportsequencingdnaseqbioconductorbioconductor-packagebioinformaticscopy-number-variationgenomicsgenomics-visualization

6.24 score 6 stars 2 packages 16 scripts 261 downloads 39 exports 135 dependencies

Last updated 25 days agofrom:f1015837c8. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winOKOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winOKOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:colByCopyNumbercomputeHclustPlotOrderEnsemblStylegetBAFColumngetChrColumngetColumngetCopyNumberColorsgetCopyNumberColumngetEndColumngetIDColumngetLOHColumngetLRRColumngetPosColumngetSegmentValueColumngetStartColumnloadCopyNumberCallsloadCopyNumberCallsCnmopsloadCopyNumberCallsCNVkitloadCopyNumberCallsDECoNloadCopyNumberCallsDNAcopyloadCopyNumberCallsPanelcnmopsloadCopyNumberCallspennCNVloadCopyNumberCallsSegloadSNPDataloadSNPDataDNAcopyloadSNPDataFromVCFplotBAFplotCopyNumberCallsplotCopyNumberCallsAsLinesplotCopyNumberSummaryplotLRRplotSingleCellCopyNumberCallsplotSingleCellCopyNumberSummaryprepareLabelsreadHDF5ZtreeremoveNAstransformChrUCSCStyleZtree2Hclust

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbamsignalsbase64encbezierBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercn.mopscodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestensembldbevaluatefansifarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonlitekaryoploteRKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngProtGenericsR6rappdirsRColorBrewerRcppRCurlregioneRrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLXVectoryamlzlibbioc

CopyNumberPlots: create copy-number specific plots using karyoploteR

Bernat Gel ([email protected]); Miriam Magallon ([email protected])

Rendered fromCopyNumberPlots.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2021-10-21
Started: 2019-03-28

Readme and manuals

Help Manual

Help pageTopics
colByCopyNumbercolByCopyNumber
computeHclustPlotOrdercomputeHclustPlotOrder
EnsemblStyleEnsemblStyle
getBAFColumngetBAFColumn
getChrColumngetChrColumn
getColumngetColumn
getCopyNumberColorsgetCopyNumberColors
getCopyNumberColumngetCopyNumberColumn
getEndColumngetEndColumn
getIDColumngetIDColumn
getLOHColumngetLOHColumn
getLRRColumngetLRRColumn
getPosColumngetPosColumn
getSegmentValueColumngetSegmentValueColumn
getStartColumngetStartColumn
loadCopyNumberCallsloadCopyNumberCalls
loadCopyNumberCallsCnmopsloadCopyNumberCallsCnmops
loadCopyNumberCallsCNVkitloadCopyNumberCallsCNVkit
loadCopyNumberCallsDECoNloadCopyNumberCallsDECoN
loadCopyNumberCallsDNAcopyloadCopyNumberCallsDNAcopy
loadCopyNumberCallsPanelcnmopsloadCopyNumberCallsPanelcnmops
loadCopyNumberCallspennCNVloadCopyNumberCallspennCNV
loadCopyNumberCallsSegloadCopyNumberCallsSeg
loadSNPDataloadSNPData
loadSNPDataDNAcopyloadSNPDataDNAcopy
loadSNPDataFromVCFloadSNPDataFromVCF
plotBAFplotBAF
plotCopyNumberCallsplotCopyNumberCalls
plotCopyNumberCallsAsLinesplotCopyNumberCallsAsLines
plotCopyNumberSummaryplotCopyNumberSummary
plotLRRplotLRR
plotSingleCellCopyNumberCallsplotSingleCellCopyNumberCalls
plotSingleCellCopyNumberSummaryplotSingleCellCopyNumberSummary
prepareLabelsprepareLabels
readHDF5ZtreereadHDF5Ztree
removeNAsremoveNAs
transformChrtransformChr
UCSCStyleUCSCStyle
Ztree2HclustZtree2Hclust