Files in KarchinLab/pictograph
Tools for modeling clonal evolution of a cancer
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/MCMC-clustering.R
R/MCMC-main.R
R/MCMC-process-clusters.R
R/MCMC_plot_clusters.R
R/calculate-BIC.R
R/estimate-multiplicity.R
R/pictograph-package.R
R/preprocessing.R
R/sample-presence.R
R/simulation.R
R/subclone-proportion.R
R/tree-gabowmyers.R
R/tree-plot.R
R/tree-score.R
README.md
inst/extdata/example1_snv.csv
inst/extdata/example1_snv_with_purity.csv
inst/extdata/example2_snv.csv
inst/extdata/example2_snv_with_purity.csv
inst/extdata/model.jags
inst/extdata/model_K1.jags
inst/extdata/output/all_trees/tree1.csv
inst/extdata/output/all_trees/tree1.png
inst/extdata/output/all_trees/tree_1_purity.csv
inst/extdata/output/all_trees/tree_1_subclone_proportion.csv
inst/extdata/output/all_trees/tree_1_subclone_proportion.png
inst/extdata/output/clusterAssign.csv
inst/extdata/output/icn_all.csv
inst/extdata/output/mcf.csv
inst/extdata/output/mcf.png
inst/extdata/output/multiplicity_all.csv
inst/extdata/output/purity.csv
inst/extdata/output/subclone_proportion.csv
inst/extdata/output/subclone_props.png
inst/extdata/output/tree.csv
inst/extdata/output/tree.png
inst/extdata/output/tree_ensemble.png
inst/extdata/output/upsetR.png
man/allThreshes.Rd
man/calcSubcloneProportions.Rd
man/calcTreeScores.Rd
man/calculateTreeScoreMutations.Rd
man/collectBestKChains.Rd
man/colorScheme.Rd
man/enumerateSpanningTreesModified.Rd
man/estimateClusterAssignments.Rd
man/estimateICN.Rd
man/estimateMCFs.Rd
man/estimateMultiplicity.Rd
man/filterEdgesBasedOnCCFs.Rd
man/generateAllTrees.Rd
man/importFiles.Rd
man/importMutationFileOnly.Rd
man/mcmcMain.Rd
man/mergeSetChains.Rd
man/pictograph-package.Rd
man/plotAllTrees.Rd
man/plotChainsMCF.Rd
man/plotClusterAssignmentProbVertical.Rd
man/plotEnsembleTree.Rd
man/plotMCFViolin.Rd
man/plotSubcloneBar.Rd
man/plotSubclonePie.Rd
man/plotTree.Rd
man/prepareGraph.Rd
man/runMCMCForAllBoxes.Rd
man/separateMutationsBySamplePresence.Rd
man/writeClusterAssignmentsTable.Rd
man/writeClusterMCFsTable.Rd
man/writeIcnTable.Rd
man/writeMultiplicityTable.Rd
man/writeSetKTable.Rd
tests/testthat.R
tests/testthat/test_number_clusters.R
tests/testthat/test_simulation.R
vignettes/.gitignore
vignettes/pictograph.Rmd
