Files in caravagnalab/basilica
bascule
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/pr-commands.yaml
.github/workflows/test-coverage.yaml
.gitignore
.idea/basilica.iml
.idea/modules.xml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/bascule-package.R
R/checks.R
R/clustering.R
R/configure_environment.R
R/data.R
R/fit.R
R/getters.R
R/getters_QC.R
R/nmf.R
R/plot_QC.R
R/plot_clustering_QC.R
R/plot_exposures.R
R/plot_fit.R
R/plot_mutations.R
R/plot_other.R
R/plot_signatures.R
R/plot_similarity.R
R/print_S3.R
R/utils_cls_analysis.R
R/utils_clustering.R
R/utils_environment.R
R/utils_fit.R
R/utils_plot.R
R/utils_py.R
R/utils_qc.R
R/utils_refine.R
R/zzz.R
README.Rmd
README.md
_config.yml
_pkgdown.yml
bascule.Rproj
codecov.yml
data/COSMIC_cn.rda
data/COSMIC_dbs.rda
data/COSMIC_indels.rda
data/COSMIC_sbs.rda
data/COSMIC_sbs_filt.rda
data/Degasperi_DBS.rda
data/Degasperi_SBS.rda
data/breast_data.rda
data/synthetic_data.rda
logo.png
man/COSMIC_cn.Rd
man/COSMIC_dbs.Rd
man/COSMIC_indels.Rd
man/COSMIC_sbs.Rd
man/COSMIC_sbs_filt.Rd
man/Degasperi_DBS.Rd
man/Degasperi_SBS.Rd
man/bascule-package.Rd
man/breast_data.Rd
man/configure_environment.Rd
man/convert_dn_names.Rd
man/fit.Rd
man/fit_clustering.Rd
man/get_denovo_signames.Rd
man/get_denovo_signatures.Rd
man/get_exposure.Rd
man/get_fixed_signames.Rd
man/get_fixed_signatures.Rd
man/get_input.Rd
man/get_signames.Rd
man/get_signatures.Rd
man/have_loaded_env.Rd
man/have_python_deps.Rd
man/load_conda_env.Rd
man/merge_clusters.Rd
man/plot.bascule_obj.Rd
man/plot_centroids.Rd
man/plot_data.Rd
man/plot_exposures.Rd
man/plot_fit.Rd
man/plot_gradient_norms.Rd
man/plot_posterior_probs.Rd
man/plot_scores.Rd
man/plot_signatures.Rd
man/plot_similarity_reference.Rd
man/print.bascule_obj.Rd
man/refine_denovo_signatures.Rd
man/synthetic_data.Rd
man/which_conda_env.Rd
vignettes/.gitignore
vignettes/articles/Fit_breast_data.Rmd
vignettes/articles/Inference.Rmd
vignettes/bascule.Rmd
