Package: BubbleTree 2.42.0

Todd Creasy

BubbleTree: BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data

CNV analysis in groups of tumor samples.

Authors:Wei Zhu <[email protected]>, Michael Kuziora <[email protected]>, Todd Creasy <[email protected]>, Brandon Higgs <[email protected]>

BubbleTree_2.42.0.tar.gz
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BubbleTree_2.42.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
BubbleTree/json (API)
NEWS

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

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

copynumbervariationsoftwaresequencingcoverage

2.18 score 17 scripts 344 downloads 3 mentions 21 exports 136 dependencies

Last updated from:d1f84961d7 (on RELEASE_3_23). Checks:1 WARNING, 8 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING236
linux-devel-x86_64ERROR471
source / vignettesERROR355
linux-release-x86_64ERROR459
macos-release-arm64ERROR325
macos-oldrel-arm64ERROR339
windows-develERROR379
windows-releaseERROR362
windows-oldrelERROR365
wasm-releaseOK175

Exports:annoByGenesAndCytoAnnotatebafTrackbtcomparebtpredictBTreePlotterBTreePredictordrawBTreedrawBubblesdrawFeaturesgetTracksheteroLociTrackinfoloadRBDmakeRBDRBDRscoreTracksaveXLStrackBTreeTrackPlotterxyTrack

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiocStyleBiostringsbiovizBasebitbit64bitopsblobbookdownBSgenomebslibcachemcheckmatecigarilloclasscliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestdplyre1071ensembldbevaluatefarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablegtoolshighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpillarpkgconfigplyrpngProtGenericsproxyR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrWriteXLSxfunXMLXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
all.somatic.lstall.somatic.lst
allCall.lstallCall.lst
allCNV.lstallCNV.lst
allHetero.lstallHetero.lst
allRBD.lstallRBD.lst
annoByGenesAndCytoannoByGenesAndCyto annoByGenesAndCyto,Annotate-method
AnnotateAnnotate-package Annotate
bafTrackbafTrack bafTrack,TrackPlotter-method
btcomparebtcompare
btpredictbtpredict btpredict,BTreePredictor-method
BTreePlotterBTreePlotter-package BTreePlotter
BTreePredictorBTreePredictor-package BTreePredictor
cancer.genes.minus2.rdacancer.genes.minus2
centromere.datcentromere.dat
cnv.grcnv.gr
cyto.grcyto.gr
drawBTreedrawBTree drawBTree,BTreePlotter-method
drawBubblesdrawBubbles drawBubbles,BTreePlotter-method
drawFeaturesdrawFeatures drawFeatures,BTreePlotter-method
gene.uni.clean.grgene.uni.clean.gr
getTracksgetTracks
heteroLociTrackheteroLociTrack heteroLociTrack,TrackPlotter-method
hg19.seqinfo.Rdhg19.seqinfo
infoinfo info,BTreePredictor-method
loadRBDloadRBD loadRBD,BTreePredictor-method
makeRBDmakeRBD makeRBD,RBD-method
mergeSnpCnvmergeSnpCnv mergeSnpCnv,RBD-method
RBDRBD-package RBD
RscoreTrackRscoreTrack RscoreTrack,TrackPlotter-method
saveXLSsaveXLS
snp.grsnp.gr
trackBTreetrackBTree trackBTree,BTreePlotter-method
TrackPlotterTrackPlotter-package TrackPlotter
vol.genesvol.genes
xyTrackxyTrack xyTrack,TrackPlotter-method