BubbleTree: BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
Version 2.6.0

CNV analysis in groups of tumor samples.

AuthorWei Zhu <zhuw@medimmune.com>, Michael Kuziora <kuzioram@medimmune.com>, Todd Creasy <creasyt@medimmune.com>, Brandon Higgs <higgsb@medimmune.com>
Bioconductor views CopyNumberVariation Coverage Sequencing Software
Date of publicationNone
MaintainerTodd Creasy <creasyt@medimmune.com>, Wei Zhu <weizhu365@gmail.com>, Kui Shen <shenk@medimmune.com>
LicenseLGPL (>= 3)
Version2.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BubbleTree")

Getting started

BubbleTree Tutorial

Popular man pages

allCNV.lst: allCNV.lst
bafTrack: bafTrack
btcompare: btcompare
cnv.gr: cnv.gr
cyto.gr: cyto.gr
hg19.seqinfo: hg19.seqinfo.Rd
mergeSnpCnv: mergeSnpCnv
See all...

All man pages Function index File listing

Man pages

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

Functions

Annotate Man page
Annotate-package Man page
BTreePlotter Man page
BTreePlotter-package Man page
BTreePredictor Man page
BTreePredictor-package Man page
RBD Man page
RBD-package Man page
RscoreTrack Man page
RscoreTrack,TrackPlotter-method Man page
TrackPlotter Man page
TrackPlotter-package Man page
all.somatic.lst Man page
allCNV.lst Man page
allCall.lst Man page
allHetero.lst Man page
allRBD.lst Man page
annoByGenesAndCyto Man page
annoByGenesAndCyto,Annotate-method Man page
bafTrack Man page
bafTrack,TrackPlotter-method Man page
btcompare Man page Source code
btpredict Man page
btpredict,BTreePredictor-method Man page
cancer.genes.minus2 Man page
centromere.dat Man page
cnv.gr Man page
cyto.gr Man page
dat2gr Source code
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 Source code
heteroLociTrack Man page
heteroLociTrack,TrackPlotter-method Man page
hg19.seqinfo Man page
info Man page
info,BTreePredictor-method Man page
keep24chr Source code
loadRBD Man page
loadRBD,BTreePredictor-method Man page
makeRBD Man page
makeRBD,RBD-method Man page
mergeSnpCnv Man page
mergeSnpCnv,RBD-method Man page
saveXLS Man page Source code
snp.gr Man page
trackBTree Man page
trackBTree,BTreePlotter-method Man page
vol.genes Man page
xyTrack Man page
xyTrack,TrackPlotter-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/Annotate.R
R/BTreePlotter.R
R/BTreePredictor.R
R/RBD.R
R/TrackPlotter.R
R/Utils.R
Rprofile
build
build/vignette.rds
data
data/all.somatic.lst.RData
data/allCNV.lst.RData
data/allCall.lst.RData
data/allHetero.lst.RData
data/allRBD.lst.RData
data/cancer.genes.minus2.rda
data/centromere.dat.rda
data/cnv.gr.rda
data/cyto.gr.rda
data/datalist
data/gene.uni.clean.gr.rda
data/hg19.seqinfo.rda
data/snp.gr.rda
data/vol.genes.rda
examples
examples/RscoreTrack-Ex.R
examples/annoByGenesAndCyto-Ex.R
examples/bafTrack-Ex.R
examples/btcompare-Ex.R
examples/btpredict-Ex.R
examples/drawBTree-Ex.R
examples/drawBubbles-Ex.R
examples/drawFeatures-Ex.R
examples/getTracks-Ex.R
examples/heteroLociTrack-Ex.R
examples/info-Ex.R
examples/loadRBD-Ex.R
examples/makeRBD-Ex.R
examples/saveXLS-Ex.R
examples/trackBTree-Ex.R
examples/xyTrack-Ex.R
inst
inst/NEWS
inst/doc
inst/doc/BubbleTree-vignette.R
inst/doc/BubbleTree-vignette.Rmd
inst/doc/BubbleTree-vignette.html
man
man/Annotate.Rd
man/BTreePlotter.Rd
man/BTreePredictor.Rd
man/RBD.Rd
man/RscoreTrack.Rd
man/TrackPlotter.Rd
man/all.somatic.lst.Rd
man/allCNV.lst.Rd
man/allCall.lst.Rd
man/allHetero.lst.Rd
man/allRBD.lst.Rd
man/annoByGenesAndCyto.Rd
man/bafTrack.Rd
man/btcompare.Rd
man/btpredict.Rd
man/cancer.genes.minus2.Rd
man/centromere.dat.Rd
man/cnv.gr.Rd
man/cyto.gr.Rd
man/drawBTree.Rd
man/drawBubbles.Rd
man/drawFeatures.Rd
man/gene.uni.clean.gr.Rd
man/getTracks.Rd
man/heteroLociTrack.Rd
man/hg19.seqinfo.Rd
man/info.Rd
man/loadRBD.Rd
man/makeRBD.Rd
man/mergeSnpCnv.Rd
man/saveXLS.Rd
man/snp.gr.Rd
man/trackBTree.Rd
man/vol.genes.Rd
man/xyTrack.Rd
vignettes
vignettes/BubbleTree-vignette.Rmd
vignettes/figures
vignettes/figures/HCC11_Primary_with_ann.png
BubbleTree documentation built on May 20, 2017, 10:27 p.m.

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