Package: BubbleTree 2.37.0
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:
BubbleTree_2.37.0.tar.gz
BubbleTree_2.37.0.zip(r-4.5)BubbleTree_2.37.0.zip(r-4.4)BubbleTree_2.37.0.zip(r-4.3)
BubbleTree_2.37.0.tgz(r-4.4-any)BubbleTree_2.37.0.tgz(r-4.3-any)
BubbleTree_2.37.0.tar.gz(r-4.5-noble)BubbleTree_2.37.0.tar.gz(r-4.4-noble)
BubbleTree_2.37.0.tgz(r-4.4-emscripten)BubbleTree_2.37.0.tgz(r-4.3-emscripten)
BubbleTree.pdf |BubbleTree.html✨
BubbleTree/json (API)
NEWS
| # Install 'BubbleTree' in R: |
| install.packages('BubbleTree', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- all.somatic.lst - All.somatic.lst
- allCNV.lst - AllCNV.lst
- allCall.lst - AllCall.lst
- allHetero.lst - AllHetero.lst
- allRBD.lst - AllRBD.lst
- cancer.genes.minus2 - Cancer.genes.minus2.rda
- centromere.dat - Centromere.dat
- cnv.gr - Cnv.gr
- cyto.gr - Cyto.gr
- gene.uni.clean.gr - Gene.uni.clean.gr
- hg19.seqinfo - Hg19.seqinfo.Rd
- snp.gr - Snp.gr
- vol.genes - Vol.genes
On BioConductor:BubbleTree-2.35.0(bioc 3.20)BubbleTree-2.34.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
copynumbervariationsoftwaresequencingcoverage
Last updated 25 days agofrom:19789a56c5. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | NOTE | Oct 30 2024 |
| R-4.3-mac | NOTE | Oct 30 2024 |
Exports:annoByGenesAndCytoAnnotatebafTrackbtcomparebtpredictBTreePlotterBTreePredictordrawBTreedrawBubblesdrawFeaturesgetTracksheteroLociTrackinfoloadRBDmakeRBDRBDRscoreTracksaveXLStrackBTreeTrackPlotterxyTrack
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiocStyleBiostringsbiovizBasebitbit64bitopsblobbookdownBSgenomebslibcachemcheckmateclasscliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestdplyre1071ensembldbevaluatefansifarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablegtoolshighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrplyrpngProtGenericsproxyR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrWriteXLSxfunXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| all.somatic.lst | all.somatic.lst |
| allCall.lst | allCall.lst |
| allCNV.lst | allCNV.lst |
| allHetero.lst | allHetero.lst |
| allRBD.lst | allRBD.lst |
| annoByGenesAndCyto | annoByGenesAndCyto annoByGenesAndCyto,Annotate-method |
| Annotate | Annotate-package Annotate |
| bafTrack | bafTrack bafTrack,TrackPlotter-method |
| btcompare | btcompare |
| btpredict | btpredict btpredict,BTreePredictor-method |
| BTreePlotter | BTreePlotter-package BTreePlotter |
| BTreePredictor | BTreePredictor-package BTreePredictor |
| cancer.genes.minus2.rda | cancer.genes.minus2 |
| centromere.dat | centromere.dat |
| cnv.gr | cnv.gr |
| cyto.gr | cyto.gr |
| drawBTree | drawBTree drawBTree,BTreePlotter-method |
| drawBubbles | drawBubbles drawBubbles,BTreePlotter-method |
| drawFeatures | drawFeatures drawFeatures,BTreePlotter-method |
| gene.uni.clean.gr | gene.uni.clean.gr |
| getTracks | getTracks |
| heteroLociTrack | heteroLociTrack heteroLociTrack,TrackPlotter-method |
| hg19.seqinfo.Rd | hg19.seqinfo |
| info | info info,BTreePredictor-method |
| loadRBD | loadRBD loadRBD,BTreePredictor-method |
| makeRBD | makeRBD makeRBD,RBD-method |
| mergeSnpCnv | mergeSnpCnv mergeSnpCnv,RBD-method |
| RBD | RBD-package RBD |
| RscoreTrack | RscoreTrack RscoreTrack,TrackPlotter-method |
| saveXLS | saveXLS |
| snp.gr | snp.gr |
| trackBTree | trackBTree trackBTree,BTreePlotter-method |
| TrackPlotter | TrackPlotter-package TrackPlotter |
| vol.genes | vol.genes |
| xyTrack | xyTrack xyTrack,TrackPlotter-method |