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