Files in hdng/clonevol
Clonal ordering and visualization
DESCRIPTION
LICENSE
NAMESPACE
R/boxplot.r
R/clonevol.r
R/clonevol2fishplot.r
R/examples.r
R/generate.boot.r
R/io.r
R/stat.r
R/trees.package.r
R/trees.r
R/utils.r
R/wrappers.r
README.md
clonevol.Rproj
data/aml1.rda
examples/aml1.r
images/AML31-small.png
images/clonevol.colors.jpg
images/fig1-AML1.jpg
images/model.png
images/variants.jitter.png
man/adjust.clone.vaf.Rd
man/assign.events.to.clones.Rd
man/assign.events.to.clones.of.a.tree.Rd
man/boot.vaf.ci.Rd
man/clone.vaf.diff.Rd
man/compare.clone.trees.Rd
man/compare.clone.trees.removing.leaves.Rd
man/convert.clone.to.branch.Rd
man/convert.consensus.tree.clone.to.branch.Rd
man/createFishPlotObjects.Rd
man/cross.rule.score.Rd
man/cutBigValue.Rd
man/determine.subclone.Rd
man/draw.branch.Rd
man/draw.clone.Rd
man/draw.sample.clones.Rd
man/draw.sample.clones.all.Rd
man/enumerate.clones.Rd
man/estimate.ccf.Rd
man/estimate.clone.vaf.Rd
man/extract.mapped.events.Rd
man/find.matched.models.Rd
man/generate.boot.Rd
man/generate.boot.nonparametric.Rd
man/generate.cloud.of.cells.Rd
man/generate.fill.points.Rd
man/generateFishplotInputs.Rd
man/germinate.Rd
man/get.cell.frac.ci.Rd
man/get.clonevol.colors.Rd
man/get.model.max.p.value.Rd
man/get.model.non.negative.ccf.prob.Rd
man/get.subclones.across.samples.Rd
man/import.tree.Rd
man/infer.clonal.models.Rd
man/insert.lf.Rd
man/is.ancestor.Rd
man/make.clonal.data.frame.Rd
man/make.graph.Rd
man/match.sample.clones.Rd
man/merge.all.matched.clone.trees.Rd
man/merge.clone.trees.Rd
man/merge.samples.Rd
man/merge.variants.and.events.Rd
man/plot.all.trees.clone.as.branch.Rd
man/plot.cell.population.Rd
man/plot.clonal.models.Rd
man/plot.clonevol.colors.Rd
man/plot.cloud.of.cells.Rd
man/plot.cluster.flow.Rd
man/plot.pairwise.Rd
man/plot.plant.Rd
man/plot.tree.Rd
man/plot.tree.clone.as.branch.Rd
man/plot.variant.clusters.Rd
man/replaceNA.Rd
man/rescale.vaf.Rd
man/save.clonevol.results.Rd
man/scale.cell.frac.Rd
man/scale.sample.position.Rd
man/set.position.Rd
man/subclonal.test.Rd
man/transfer.events.to.consensus.trees.Rd
man/trim.clone.trees.Rd
man/write.tree.Rd
simulations/README
simulations/run.sh
simulations/sim.r
simulations/truth/AC1D0S0
simulations/truth/AC1D0S1
simulations/truth/AC1D1S0
simulations/truth/AC1D1S1
simulations/truth/AC2D0S0
simulations/truth/AC2D0S1
simulations/truth/AC2D1S0
simulations/truth/AC2D1S1
simulations/truth/AC3D0S0
simulations/truth/AC3D0S1
simulations/truth/AC3D1S0
simulations/truth/AC3D1S1
simulations/truth/BC1D0S0
simulations/truth/BC1D0S1
simulations/truth/BC1D1S0
simulations/truth/BC1D1S1
simulations/truth/BC2D0S0
simulations/truth/BC2D0S1
simulations/truth/BC2D1S0
simulations/truth/BC2D1S1
simulations/truth/BC3D0S0
simulations/truth/BC3D0S1
simulations/truth/BC3D1S0
simulations/truth/BC3D1S1
vignettes/aml1_all.png
vignettes/aml1_clusters.png
vignettes/clonevol.Rmd
vignettes/clonevol.pdf
vignettes/clonevol.png
vignettes/refs.bib
