Man pages for caravagnalab/basilica
bascule
| bascule-package | bascule: bascule |
| breast_data | Analysis of breast tumours |
| configure_environment | Configure the reticulate environment |
| convert_dn_names | Function to map de novo signatures to input catalogues |
| COSMIC_cn | COSMIC catalogue for CN (version 3.4, GRCh37) |
| COSMIC_dbs | COSMIC catalogue for DBS (version 3.4, GRCh37) |
| COSMIC_indels | COSMIC catalogue for Indels (version 3.4, GRCh37) |
| COSMIC_sbs | COSMIC catalogue for SBS (version 3.4, GRCh37) |
| COSMIC_sbs_filt | COSMIC catalogue for SBS filtered (version 3.4, GRCh37) |
| Degasperi_DBS | Degasperi DBS catalogue |
| Degasperi_SBS | Degasperi SBS catalogue |
| fit | Fit a bascule object |
| fit_clustering | Fit clustering |
| get_denovo_signames | Get denovo signatures names |
| get_denovo_signatures | Get de novo (reference) signatures |
| get_exposure | Get exposures |
| get_fixed_signames | Get reference signatures names |
| get_fixed_signatures | Get fixed (reference) signatures |
| get_input | Get input data |
| get_signames | Get signatures names |
| get_signatures | Get signatures |
| have_loaded_env | Check if there is a loaded 'conda' environment. |
| have_python_deps | Check if 'Python' packages are installed in the environment. |
| load_conda_env | Load the input 'conda' environment. |
| merge_clusters | Function to merge similar clusters |
| plot.bascule_obj | Plot for class "bascule_obj". |
| plot_centroids | Plot clustering centroids |
| plot_data | Function to visualize the input and reconstructed mutation... |
| plot_exposures | Function to visualize the estimated exposures |
| plot_fit | Report of the fit |
| plot_gradient_norms | Plot parameters gradients norms |
| plot_posterior_probs | Plot posterior probabilities |
| plot_scores | Plot model selection scores |
| plot_signatures | Function to visualize the estimated and reference signatures. |
| plot_similarity_reference | Function to visualize the similarity of denovo and reference... |
| print.bascule_obj | Print for class "bascule_obj". |
| refine_denovo_signatures | De novo signatures refinement. |
| synthetic_data | Analysis of a synthetic cohort |
| which_conda_env | Retrieve the name of the currently loaded environment. |
