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).

Author
Wei Zhu <zhuw@medimmune.com>, Michael Kuziora <kuzioram@medimmune.com>, Todd Creasy <creasyt@medimmune.com>, Brandon Higgs <higgsb@medimmune.com>
Date of publication
None
Maintainer
Todd Creasy <creasyt@medimmune.com>, Wei Zhu <weizhu365@gmail.com>
License
LGPL (>= 3)
Version
2.4.0

View on Bioconductor

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

Files in this package

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