Files in caravagnalab/lineaGT
lineaGT
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/S3_methods_plots.R
R/S3_methods_print.R
R/add_elements_to_object.R
R/check_inputs.R
R/configure_environment.R
R/data.R
R/dataset_filtering.R
R/datasets_reshaping.R
R/diagnostics.R
R/fit_model.R
R/generate_synthetic_df.R
R/getter_dataframe.R
R/getter_params.R
R/growth_model.R
R/init_object.R
R/mutations_clust.R
R/phylogenies_inference.R
R/plots_coverage.R
R/plots_diagn.R
R/plots_differentiation_tree.R
R/plots_growth.R
R/plots_mullerplot.R
R/plots_phylogenies.R
R/plots_vaf.R
R/utils.R
R/utils_differentiation.R
R/utils_environment.R
R/utils_fit.R
R/utils_getter.R
R/utils_growth_model.R
R/utils_mullerplot.R
R/utils_mullerplot_df.R
R/utils_mutations.R
R/zzz.R
README.Rmd
README.md
_config.yml
_pkgdown.yml
data/cov.df.example.rda
data/vaf.df.example.rda
data/x.example.rda
docs/.nojekyll
docs/404.html
docs/LICENSE-text.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/Get-started.html
docs/articles/Input-formats.html
docs/articles/Lineage-inference.html
docs/articles/Plotting-functions.html
docs/articles/Utilities.html
docs/articles/articles/Get-started.html
docs/articles/articles/Input-formats.html
docs/articles/articles/Lineage-inference.html
docs/articles/articles/Plotting-functions.html
docs/articles/articles/Utilities.html
docs/articles/index.html
docs/authors.html
docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js
docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.1.0/bootstrap.min.css
docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js
docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.1.3/bootstrap.min.css
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.2.2/bootstrap.min.css
docs/deps/data-deps.txt
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/add_vaf.html
docs/reference/configure_environment.html
docs/reference/cov.df.example.html
docs/reference/figures/logo.jpg
docs/reference/figures/logo.png
docs/reference/filter_dataset.html
docs/reference/fit.html
docs/reference/fit_growth_rates.html
docs/reference/fit_mutations.html
docs/reference/fit_phylogenies.html
docs/reference/get_ISs.html
docs/reference/get_cov_dataframe.html
docs/reference/get_covariance_Cholesky.html
docs/reference/get_covariance_Sigma.html
docs/reference/get_dataframe.html
docs/reference/get_dimensions.html
docs/reference/get_labels.html
docs/reference/get_lineages.html
docs/reference/get_mean.html
docs/reference/get_sigma.html
docs/reference/get_timepoints.html
docs/reference/get_unique_labels.html
docs/reference/get_unique_muts_labels.html
docs/reference/get_vaf_dataframe.html
docs/reference/get_viber_clusters.html
docs/reference/get_weights.html
docs/reference/get_z_probs.html
docs/reference/have_loaded_env.html
docs/reference/have_python_deps.html
docs/reference/index.html
docs/reference/load_conda_env.html
docs/reference/plot.mvnmm.html
docs/reference/plot_IC.html
docs/reference/plot_differentiation_tree.html
docs/reference/plot_exp_fit.html
docs/reference/plot_exp_rate.html
docs/reference/plot_gradient_norms.html
docs/reference/plot_growth_rates.html
docs/reference/plot_growth_regression.html
docs/reference/plot_losses.html
docs/reference/plot_marginal.html
docs/reference/plot_mixture_weights.html
docs/reference/plot_mullerplot.html
docs/reference/plot_phylogeny.html
docs/reference/plot_scatter_density.html
docs/reference/plot_vaf.html
docs/reference/plot_vaf_time.html
docs/reference/print.mvnmm.html
docs/reference/run_viber.html
docs/reference/vaf.df.example.html
docs/reference/which_conda_env.html
docs/reference/x.example.html
docs/search.json
docs/sitemap.xml
lineaGT.Rproj
logo.png
man/configure_environment.Rd
man/cov.df.example.Rd
man/estimate_n_pops.Rd
man/figures/logo.jpg
man/figures/logo.png
man/filter_dataset.Rd
man/fit.Rd
man/fit_growth_rates.Rd
man/fit_mutations.Rd
man/fit_phylogenies.Rd
man/get_ISs.Rd
man/get_cov_dataframe.Rd
man/get_covariance_Cholesky.Rd
man/get_covariance_Sigma.Rd
man/get_dimensions.Rd
man/get_labels.Rd
man/get_lineages.Rd
man/get_mean.Rd
man/get_sigma.Rd
man/get_timepoints.Rd
man/get_unique_labels.Rd
man/get_unique_muts_labels.Rd
man/get_vaf_dataframe.Rd
man/get_weights.Rd
man/get_z_probs.Rd
man/have_loaded_env.Rd
man/have_python_deps.Rd
man/load_conda_env.Rd
man/plot.mvnmm.Rd
man/plot_IC.Rd
man/plot_differentiation_tree.Rd
man/plot_gradient_norms.Rd
man/plot_growth_rates.Rd
man/plot_growth_regression.Rd
man/plot_losses.Rd
man/plot_marginal.Rd
man/plot_mixture_weights.Rd
man/plot_mullerplot.Rd
man/plot_phylogeny.Rd
man/plot_scatter_density.Rd
man/plot_vaf.Rd
man/plot_vaf_time.Rd
man/print.mvnmm.Rd
man/vaf.df.example.Rd
man/which_conda_env.Rd
man/x.example.Rd
nobuild/Lineage-inference.Rmd
nobuild/ari_nmi_comparison.png
nobuild/simulations.last.boxplot.png
nobuild/simulations.last.swarm.png
nobuild/test_lineaGT.R
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.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/.gitignore
vignettes/articles/Inference.Rmd
vignettes/articles/Input-formats.Rmd
vignettes/articles/Plotting-functions.Rmd
vignettes/articles/Utilities.Rmd
vignettes/lineaGT.Rmd
