├── AUTHORS ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── clustering_helper_functions.R ├── example.R ├── functionsForSimpleClustering.v13.R ├── main_clustering_functions.R ├── main_conipher_run.R ├── main_treebuilding_functions.R ├── sequenza_functions.R └── treebuilding_helper_functions.R ├── README.md ├── data ├── input_table.rda └── results │ ├── CRUKTOY001.tree.RDS │ ├── pytree_and_bar.pdf │ └── pytree_multipletrees.pdf ├── inst └── extdata │ ├── input_table.tsv │ └── template.config.yaml └── man ├── calc.pyclone.ci.Rd ├── clonality.function.Rd ├── clusterDistributionAcrossGenome.Rd ├── clustering_postprocess.Rd ├── clustering_preprocess.Rd ├── clustering_run.Rd ├── color.tree.Rd ├── compute_subclonal_expansion_score.Rd ├── compute_subclone_proportions.Rd ├── compute_sum_condition_error.Rd ├── compute_tree_edge_probability.Rd ├── conipher_clustering.Rd ├── conipher_run.Rd ├── conipher_treebuilding.Rd ├── correct.clonality.nesting.Rd ├── createAllPathsList.Rd ├── determine.cluster.nesting.Rd ├── extract_consensus_relationships.Rd ├── extract_daughters.Rd ├── get_terminal_clusters.Rd ├── get_tree_level.Rd ├── grow.multi.trees.Rd ├── grow.trees.Rd ├── input_table.Rd ├── is.there.ccf.issue.Rd ├── permute.clusters.to.remove.Rd ├── process_mean_cluster_ccfs.Rd ├── prune.tree.Rd ├── remove_clustered_clones.Rd ├── test.distributions.Rd ├── treebuilding_plot.Rd ├── treebuilding_preprocess.Rd ├── treebuilding_run.Rd └── unfold_tree.Rd /AUTHORS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/McGranahanLab/CONIPHER/HEAD/AUTHORS -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/McGranahanLab/CONIPHER/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: 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