Introduction | Installation | Quick Start | Loading Copy-Number Data | Load Raw Data | Load Copy-Number Calls | Plotting Copy-Number Data | Plotting Raw Data | plotBAF | Plot LRR | Plot Copy-Number Calls | plotCopyNumberCalls | plotCopyNumberCallsAsLines | plotCopyNumberSummary | Session Info
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:
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✨
DESCRIPTION |NEWS
card.svg |card.png
CopyNumberPlots/json (API)
| # 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
Last updated from:c6b9987bd3. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 354 | ||
| linux-devel-x86_64 | NOTE | 501 | ||
| source / vignettes | OK | 422 | ||
| linux-release-x86_64 | NOTE | 511 | ||
| macos-release-arm64 | NOTE | 310 | ||
| macos-oldrel-arm64 | NOTE | 260 | ||
| windows-devel | NOTE | 434 | ||
| windows-release | NOTE | 416 | ||
| windows-oldrel | NOTE | 424 | ||
| wasm-release | OK | 301 |
Exports:colByCopyNumbercomputeHclustPlotOrderEnsemblStylegetBAFColumngetChrColumngetColumngetCopyNumberColorsgetCopyNumberColumngetEndColumngetIDColumngetLOHColumngetLRRColumngetPosColumngetSegmentValueColumngetStartColumnloadCopyNumberCallsloadCopyNumberCallsCnmopsloadCopyNumberCallsCNVkitloadCopyNumberCallsDECoNloadCopyNumberCallsDNAcopyloadCopyNumberCallsPanelcnmopsloadCopyNumberCallspennCNVloadCopyNumberCallsSegloadSNPDataloadSNPDataDNAcopyloadSNPDataFromVCFplotBAFplotCopyNumberCallsplotCopyNumberCallsAsLinesplotCopyNumberSummaryplotLRRplotSingleCellCopyNumberCallsplotSingleCellCopyNumberSummaryprepareLabelsreadHDF5ZtreeremoveNAstransformChrUCSCStyleZtree2Hclust
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbamsignalsbase64encbezierBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercn.mopscodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestdir.expiryensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonlitekaryoploteRKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpkgconfigpngProtGenericsR6rappdirsRColorBrewerRcppRCurlregioneRrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| colByCopyNumber | colByCopyNumber |
| computeHclustPlotOrder | computeHclustPlotOrder |
| EnsemblStyle | EnsemblStyle |
| getBAFColumn | getBAFColumn |
| getChrColumn | getChrColumn |
| getColumn | getColumn |
| getCopyNumberColors | getCopyNumberColors |
| getCopyNumberColumn | getCopyNumberColumn |
| getEndColumn | getEndColumn |
| getIDColumn | getIDColumn |
| getLOHColumn | getLOHColumn |
| getLRRColumn | getLRRColumn |
| getPosColumn | getPosColumn |
| getSegmentValueColumn | getSegmentValueColumn |
| getStartColumn | getStartColumn |
| loadCopyNumberCalls | loadCopyNumberCalls |
| loadCopyNumberCallsCnmops | loadCopyNumberCallsCnmops |
| loadCopyNumberCallsCNVkit | loadCopyNumberCallsCNVkit |
| loadCopyNumberCallsDECoN | loadCopyNumberCallsDECoN |
| loadCopyNumberCallsDNAcopy | loadCopyNumberCallsDNAcopy |
| loadCopyNumberCallsPanelcnmops | loadCopyNumberCallsPanelcnmops |
| loadCopyNumberCallspennCNV | loadCopyNumberCallspennCNV |
| loadCopyNumberCallsSeg | loadCopyNumberCallsSeg |
| loadSNPData | loadSNPData |
| loadSNPDataDNAcopy | loadSNPDataDNAcopy |
| loadSNPDataFromVCF | loadSNPDataFromVCF |
| plotBAF | plotBAF |
| plotCopyNumberCalls | plotCopyNumberCalls |
| plotCopyNumberCallsAsLines | plotCopyNumberCallsAsLines |
| plotCopyNumberSummary | plotCopyNumberSummary |
| plotLRR | plotLRR |
| plotSingleCellCopyNumberCalls | plotSingleCellCopyNumberCalls |
| plotSingleCellCopyNumberSummary | plotSingleCellCopyNumberSummary |
| prepareLabels | prepareLabels |
| readHDF5Ztree | readHDF5Ztree |
| removeNAs | removeNAs |
| transformChr | transformChr |
| UCSCStyle | UCSCStyle |
| Ztree2Hclust | Ztree2Hclust |
