Files in caravagnalab/mobster
MOBSTER - Model-based tumour subclonal deconvolution
.Rbuildignore
.github/.gitignore
.github/workflows/check-development.yml
.github/workflows/check-master.yml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/.DS_Store
R/Clusters.R
R/Clusters_denovo.R
R/Latent_variables.R
R/Model_selection.R
R/S3_methods_plot.R
R/S3_methods_print.R
R/algorithm_fit.R
R/annotate_genes_from_locations.R
R/bootstrapped_statistics.R
R/check_input.R
R/choose_clusters.R
R/data.R
R/density.R
R/dnds.R
R/drivers.R
R/evodynamics.R
R/extract_dnds_input.R
R/get_clone_trees.R
R/heuristics.R
R/load_VCF.R
R/mobster_bootstrap.R
R/mobster_fit.R
R/output_cli.R
R/plot_NLL.R
R/plot_boostrap_Beta.R
R/plot_boostrap_coclustering.R
R/plot_boostrap_mixing_proportions.R
R/plot_boostrap_model_frequency.R
R/plot_boostrap_tail.R
R/plot_entropy.R
R/plot_fit_scores.R
R/plot_gofit.R
R/plot_init.R
R/plot_latent_variables.R
R/plot_mixing_proportions.R
R/plot_model_selection.R
R/random_dataset.R
R/to_string.R
R/utils_bootstrap.R
R/utils_dnds.R
R/utils_fit.R
R/utils_input.R
R/utils_plot.R
R/zzz.R
README.Rmd
README.md
_config.yml
_pkgdown.yml
data/.DS_Store
data/LU4_lung_sample.rda
data/LUFF76_lung_sample.rda
data/PD4120a_breast_sample.rda
data/cancer_genes_dnds.rda
data/fit_example.rda
data/subclonedynamics.rda
man/Clusters.Rd
man/Clusters_denovo.Rd
man/LU4_lung_sample.Rd
man/LUFF76_lung_sample.Rd
man/bootstrapped_statistics.Rd
man/cancer_genes_dnds.Rd
man/choose_clusters.Rd
man/ddbpmm.Rd
man/dnds.Rd
man/evolutionary_parameters.Rd
man/figures/logo.png
man/fit_example.Rd
man/get_clone_trees.Rd
man/load_vcf.Rd
man/mobster_bootstrap.Rd
man/mobster_fit.Rd
man/plot.dbpmm.Rd
man/plot_NLL.Rd
man/plot_bootstrap_Beta.Rd
man/plot_bootstrap_coclustering.Rd
man/plot_bootstrap_mixing_proportions.Rd
man/plot_bootstrap_model_frequency.Rd
man/plot_bootstrap_tail.Rd
man/plot_entropy.Rd
man/plot_fit_scores.Rd
man/plot_gofit.Rd
man/plot_init.Rd
man/plot_latent_variables.Rd
man/plot_mixing_proportions.Rd
man/plot_model_selection.Rd
man/print.dbpmm.Rd
man/random_dataset.Rd
man/rdbpmm.Rd
man/summary.dbpmm.Rd
man/to_string.Rd
nobuild/Create_lists.R
nobuild/TODO.R
nobuild/TODO2.R
nobuild/ex.R
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
vignettes/Example_tumour_simulation.html
vignettes/Example_tumour_simulation_files/figure-html/unnamed-chunk-2-1.gif
vignettes/Example_tumour_simulation_files/figure-html/unnamed-chunk-3-1.png
vignettes/a1_introduction.Rmd
vignettes/a2_plotting.Rmd
vignettes/a3_bootstrap.Rmd
vignettes/a4_popgen.Rmd
vignettes/a5_dnds.Rmd
vignettes/a6_CloneTrees.Rmd
vignettes/a7_Example_tumour_simulation.Rmd
vignettes/bootstrap_files/figure-gfm/unnamed-chunk-10-1.png
vignettes/bootstrap_files/figure-gfm/unnamed-chunk-3-1.png
vignettes/bootstrap_files/figure-gfm/unnamed-chunk-5-1.png
vignettes/bootstrap_files/figure-gfm/unnamed-chunk-8-1.png
vignettes/bootstrap_files/figure-gfm/unnamed-chunk-9-1.png
vignettes/evolutionary_analysis_files/figure-gfm/unnamed-chunk-10-1.png
vignettes/evolutionary_analysis_files/figure-gfm/unnamed-chunk-3-1.png
vignettes/evolutionary_analysis_files/figure-gfm/unnamed-chunk-6-1.png
vignettes/mobster.Rmd
vignettes/simulationdata.Rdata
vignettes/strelka-example.vcf
