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 (Publication Pending).

AuthorWei Zhu <zhuw@medimmune.com>, Michael Kuziora <kuzioram@medimmune.com>, Todd Creasy <creasyt@medimmune.com>, Brandon Higgs <higgsb@medimmune.com>
Date of publicationNone
MaintainerTodd Creasy <creasyt@medimmune.com>, Wei Zhu <weizhu365@gmail.com>
LicenseLGPL (>= 3)
Version2.4.0

View on Bioconductor

Functions

allCall.lst Man page
allCNV.lst Man page
allHetero.lst Man page
allRBD.lst Man page
all.somatic.lst Man page
annoByGenesAndCyto Man page
annoByGenesAndCyto,Annotate-method Man page
Annotate Man page
Annotate-package Man page
bafTrack Man page
bafTrack,TrackPlotter-method Man page
btcompare Man page
btpredict Man page
btpredict,BTreePredictor-method Man page
BTreePlotter Man page
BTreePlotter-package Man page
BTreePredictor Man page
BTreePredictor-package Man page
cancer.genes.minus2 Man page
centromere.dat Man page
cnv.gr Man page
cyto.gr Man page
drawBTree Man page
drawBTree,BTreePlotter-method Man page
drawBubbles Man page
drawBubbles,BTreePlotter-method Man page
drawFeatures Man page
drawFeatures,BTreePlotter-method Man page
gene.uni.clean.gr Man page
getTracks Man page
heteroLociTrack Man page
heteroLociTrack,TrackPlotter-method Man page
hg19.seqinfo Man page
info Man page
info,BTreePredictor-method Man page
loadRBD Man page
loadRBD,BTreePredictor-method Man page
makeRBD Man page
makeRBD,RBD-method Man page
mergeSnpCnv Man page
mergeSnpCnv,RBD-method Man page
RBD Man page
RBD-package Man page
RscoreTrack Man page
RscoreTrack,TrackPlotter-method Man page
saveXLS Man page
snp.gr Man page
trackBTree Man page
trackBTree,BTreePlotter-method Man page
TrackPlotter Man page
TrackPlotter-package Man page
vol.genes Man page
xyTrack Man page
xyTrack,TrackPlotter-method Man page

Files

BubbleTree/DESCRIPTION
BubbleTree/NAMESPACE
BubbleTree/R
BubbleTree/R/Annotate.R BubbleTree/R/BTreePlotter.R BubbleTree/R/BTreePredictor.R BubbleTree/R/RBD.R BubbleTree/R/TrackPlotter.R BubbleTree/R/Utils.R
BubbleTree/Rprofile
BubbleTree/build
BubbleTree/build/vignette.rds
BubbleTree/data
BubbleTree/data/all.somatic.lst.RData
BubbleTree/data/allCNV.lst.RData
BubbleTree/data/allCall.lst.RData
BubbleTree/data/allHetero.lst.RData
BubbleTree/data/allRBD.lst.RData
BubbleTree/data/cancer.genes.minus2.rda
BubbleTree/data/centromere.dat.rda
BubbleTree/data/cnv.gr.rda
BubbleTree/data/cyto.gr.rda
BubbleTree/data/datalist
BubbleTree/data/gene.uni.clean.gr.rda
BubbleTree/data/hg19.seqinfo.rda
BubbleTree/data/snp.gr.rda
BubbleTree/data/vol.genes.rda
BubbleTree/examples
BubbleTree/examples/RscoreTrack-Ex.R
BubbleTree/examples/annoByGenesAndCyto-Ex.R
BubbleTree/examples/bafTrack-Ex.R
BubbleTree/examples/btcompare-Ex.R
BubbleTree/examples/btpredict-Ex.R
BubbleTree/examples/drawBTree-Ex.R
BubbleTree/examples/drawBubbles-Ex.R
BubbleTree/examples/drawFeatures-Ex.R
BubbleTree/examples/getTracks-Ex.R
BubbleTree/examples/heteroLociTrack-Ex.R
BubbleTree/examples/info-Ex.R
BubbleTree/examples/loadRBD-Ex.R
BubbleTree/examples/makeRBD-Ex.R
BubbleTree/examples/saveXLS-Ex.R
BubbleTree/examples/trackBTree-Ex.R
BubbleTree/examples/xyTrack-Ex.R
BubbleTree/inst
BubbleTree/inst/NEWS
BubbleTree/inst/doc
BubbleTree/inst/doc/BubbleTree-vignette.R
BubbleTree/inst/doc/BubbleTree-vignette.Rmd
BubbleTree/inst/doc/BubbleTree-vignette.html
BubbleTree/man
BubbleTree/man/Annotate.Rd BubbleTree/man/BTreePlotter.Rd BubbleTree/man/BTreePredictor.Rd BubbleTree/man/RBD.Rd BubbleTree/man/RscoreTrack.Rd BubbleTree/man/TrackPlotter.Rd BubbleTree/man/all.somatic.lst.Rd BubbleTree/man/allCNV.lst.Rd BubbleTree/man/allCall.lst.Rd BubbleTree/man/allHetero.lst.Rd BubbleTree/man/allRBD.lst.Rd BubbleTree/man/annoByGenesAndCyto.Rd BubbleTree/man/bafTrack.Rd BubbleTree/man/btcompare.Rd BubbleTree/man/btpredict.Rd BubbleTree/man/cancer.genes.minus2.Rd BubbleTree/man/centromere.dat.Rd BubbleTree/man/cnv.gr.Rd BubbleTree/man/cyto.gr.Rd BubbleTree/man/drawBTree.Rd BubbleTree/man/drawBubbles.Rd BubbleTree/man/drawFeatures.Rd BubbleTree/man/gene.uni.clean.gr.Rd BubbleTree/man/getTracks.Rd BubbleTree/man/heteroLociTrack.Rd BubbleTree/man/hg19.seqinfo.Rd BubbleTree/man/info.Rd BubbleTree/man/loadRBD.Rd BubbleTree/man/makeRBD.Rd BubbleTree/man/mergeSnpCnv.Rd BubbleTree/man/saveXLS.Rd BubbleTree/man/snp.gr.Rd BubbleTree/man/trackBTree.Rd BubbleTree/man/vol.genes.Rd BubbleTree/man/xyTrack.Rd
BubbleTree/vignettes
BubbleTree/vignettes/BubbleTree-vignette.Rmd
BubbleTree/vignettes/figures
BubbleTree/vignettes/figures/HCC11_Primary_with_ann.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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