Package: CopyNumberPlots 1.29.0

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_1.29.0.tar.gz
CopyNumberPlots_1.29.0.zip(r-4.7)CopyNumberPlots_1.29.0.zip(r-4.6)CopyNumberPlots_1.29.0.zip(r-4.5)
CopyNumberPlots_1.29.0.tgz(r-4.6-any)CopyNumberPlots_1.29.0.tgz(r-4.5-any)
CopyNumberPlots_1.29.0.tar.gz(r-4.7-any)CopyNumberPlots_1.29.0.tar.gz(r-4.6-any)
CopyNumberPlots_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CopyNumberPlots/json (API)
NEWS

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

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

On BioConductor:CopyNumberPlots-1.29.0(bioc 3.24)CopyNumberPlots-1.28.0(bioc 3.23)

visualizationcopynumbervariationcoverageonechanneldataimportsequencingdnaseqbioconductorbioconductor-packagebioinformaticscopy-number-variationgenomicsgenomics-visualization

6.05 score 6 stars 1 packages 21 scripts 321 downloads 39 exports 131 dependencies

Last updated from:c6b9987bd3. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR298
linux-devel-x86_64NOTE577
source / vignettesOK352
linux-release-x86_64NOTE585
macos-release-arm64NOTE392
macos-oldrel-arm64NOTE377
windows-develNOTE458
windows-releaseNOTE505
windows-oldrelNOTE459
wasm-releaseOK207

Exports:colByCopyNumbercomputeHclustPlotOrderEnsemblStylegetBAFColumngetChrColumngetColumngetCopyNumberColorsgetCopyNumberColumngetEndColumngetIDColumngetLOHColumngetLRRColumngetPosColumngetSegmentValueColumngetStartColumnloadCopyNumberCallsloadCopyNumberCallsCnmopsloadCopyNumberCallsCNVkitloadCopyNumberCallsDECoNloadCopyNumberCallsDNAcopyloadCopyNumberCallsPanelcnmopsloadCopyNumberCallspennCNVloadCopyNumberCallsSegloadSNPDataloadSNPDataDNAcopyloadSNPDataFromVCFplotBAFplotCopyNumberCallsplotCopyNumberCallsAsLinesplotCopyNumberSummaryplotLRRplotSingleCellCopyNumberCallsplotSingleCellCopyNumberSummaryprepareLabelsreadHDF5ZtreeremoveNAstransformChrUCSCStyleZtree2Hclust

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbamsignalsbase64encbezierBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercn.mopscodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestdir.expiryensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonlitekaryoploteRKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpkgconfigpngProtGenericsR6rappdirsRColorBrewerRcppRCurlregioneRrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryaml

CopyNumberPlots: create copy-number specific plots using karyoploteR

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

Rendered fromCopyNumberPlots.Rmdusingknitr::rmarkdownon Jun 03 2026.

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