Files in caravagn/revolver
REVOLVER - Repeated Evolution in Cancer

.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md R/CCF_parser.R R/DET_index.R R/S3_plot_functions.R R/S3_print_functions.R R/color_palettes.R R/compute_clone_trees.R R/compute_mutation_trees.R R/get_features.R R/getter_functions.R R/ggplot_theme.R R/input_custom_trees.R R/plot_CCF_histogram.R R/plot_DET_index.R R/plot_cluster.R R/plot_dendrogram.R R/plot_drivers_clonality.R R/plot_drivers_graph.R R/plot_drivers_occurrence.R R/plot_jackknife_cluster_stability.R R/plot_jackknife_coclustering.R R/plot_jackknife_trajectories.R R/plot_patient_data.R R/plot_patient_mutation_burden.R R/plot_patient_oncoprint.R R/plot_patient_trees.R R/plot_patient_trees_scores.R R/plot_penalty.R R/plot_trajectories_per_clusters.R R/remove_drivers.R R/remove_patients.R R/revolver_check_cohort.R R/revolver_cluster.R R/revolver_cohort.R R/revolver_fit.R R/revolver_jackknife.R R/stats_functions.R R/utils_clustering.R R/utils_cohort.R R/utils_information_transfer.R R/utils_jackknife.R R/zzz.R README.Rmd README.md
_config.yml
_pkgdown.yml
docs/404.html
docs/articles/Cross_CRC_MSeq.html
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docs/articles/Cross_CRC_MSeq_files/header-attrs-2.7/header-attrs.js
docs/articles/FAQ.html
docs/articles/FAQ_files/header-attrs-2.7/header-attrs.js
docs/articles/Getters.html
docs/articles/Getters_files/header-attrs-2.7/header-attrs.js
docs/articles/Input_formats.html
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docs/articles/Input_formats_files/header-attrs-2.7/header-attrs.js
docs/articles/Plotting_functions.html
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docs/articles/Plotting_functions_files/header-attrs-2.7/header-attrs.js
docs/articles/index.html
docs/articles/revolver.html
docs/articles/revolver_files/header-attrs-2.7/header-attrs.js
docs/authors.html
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docs/reference/CCF.html
docs/reference/CCF_clusters.html
docs/reference/CCF_parser.html
docs/reference/Clonal_cluster.html
docs/reference/Cluster.html
docs/reference/DET_index.html
docs/reference/Data.html
docs/reference/Drivers.html
docs/reference/ITransfer.html
docs/reference/Jackknife_cluster_stability.html
docs/reference/Jackknife_patient_coclustering.html
docs/reference/Jackknife_trajectories_stability.html
docs/reference/Phylo.html
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docs/reference/Samples.html
docs/reference/Stats.html
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docs/reference/Subclonal.html
docs/reference/TRACERx_cohort.html
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docs/reference/Truncal.html
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docs/reference/compute_mutation_trees.html
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docs/reference/get_features.html
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docs/reference/plot.rev_cohort.html
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docs/reference/plot_data_mutation_burden.html
docs/reference/plot_data_oncoprint.html
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docs/reference/plot_penalty-1.png
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docs/reference/plot_penalty.html
docs/reference/plot_trajectories_per_cluster-1.png
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docs/reference/plot_trajectories_per_cluster.html
docs/reference/plot_trees.html
docs/reference/plot_trees_scores.html
docs/reference/print.rev_cohort.html
docs/reference/print.rev_cohort_fit.html
docs/reference/print.rev_phylo.html
docs/reference/remove_driver.html
docs/reference/remove_drivers.html
docs/reference/remove_patients.html
docs/reference/revolver_check_cohort.html
docs/reference/revolver_cluster.html
docs/reference/revolver_cohort.html
docs/reference/revolver_compute_CLtrees.html
docs/reference/revolver_compute_phylogenies.html
docs/reference/revolver_deletePatients.html
docs/reference/revolver_fit.html
docs/reference/revolver_jackknife.html
docs/reference/revolver_phylogeny.html
docs/reference/revolver_plt_jackknife_coclust.html
docs/reference/revolver_plt_jackknife_coclust_bplot.html
docs/reference/revolver_plt_jackknife_edge_counts.html
docs/reference/revolver_plt_jackknife_edge_prb.html
docs/reference/revolver_removeDriver.html
docs/reference/revolver_subsetDrivers.html
docs/reference/stats.rev_phylo.html
docs/reference/summary.rev_phylo.html
docs/sitemap.xml
man/CCF.Rd man/CCF_clusters.Rd man/CCF_parser.Rd man/Clonal_cluster.Rd man/Cluster.Rd man/DET_index.Rd man/Data.Rd man/Drivers.Rd man/ITransfer.Rd man/Jackknife_cluster_stability.Rd man/Jackknife_patient_coclustering.Rd man/Jackknife_trajectories_stability.Rd man/Phylo.Rd man/Samples.Rd man/Stats.Rd man/Stats_cohort.Rd man/Stats_drivers.Rd man/Stats_fits.Rd man/Stats_trees.Rd man/Subclonal.Rd man/Truncal.Rd man/compute_clone_trees.Rd man/compute_mutation_trees.Rd man/distinct_palette_few.Rd man/distinct_palette_many.Rd
man/figures/logo.png
man/get_features.Rd man/gradient_palette.Rd man/input_custom_trees.Rd man/plot.rev_cohort.Rd man/plot.rev_cohort_fit.Rd man/plot_DET_index.Rd man/plot_clusters.Rd man/plot_dendrogram.Rd man/plot_drivers_clonality.Rd man/plot_drivers_graph.Rd man/plot_drivers_occurrence.Rd man/plot_jackknife_cluster_stability.Rd man/plot_jackknife_coclustering.Rd man/plot_jackknife_trajectories_stability.Rd man/plot_patient_CCF_histogram.Rd man/plot_patient_data.Rd man/plot_patient_mutation_burden.Rd man/plot_patient_oncoprint.Rd man/plot_patient_trees.Rd man/plot_patient_trees_scores.Rd man/plot_penalty.Rd man/plot_trajectories_per_cluster.Rd man/print.rev_cohort.Rd man/print.rev_cohort_fit.Rd man/remove_drivers.Rd man/remove_patients.Rd man/revolver_check_cohort.Rd man/revolver_cluster.Rd man/revolver_cohort.Rd man/revolver_fit.Rd man/revolver_jackknife.Rd old_vignette/Getter_functions.R old_vignette/Getters.md old_vignette/Plotting_functions.Rmd old_vignette/Plotting_functions.md old_vignette/Untitled.R old_vignette/Untitled_CRC.R old_vignette/mustrun.R
pkgdown/favicon/favicon.ico
vignettes/.gitignore
vignettes/Cross_CRC_MSeq.Rmd vignettes/FAQ.Rmd vignettes/Getters.Rmd vignettes/Input_formats.Rmd vignettes/Plotting_functions.Rmd vignettes/revolver.Rmd
caravagn/revolver documentation built on May 21, 2022, 5:48 p.m.