# bascule

## Documentation for package ‘bascule’ version 1.0.1

- DESCRIPTION file.

## Help Pages

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_n_denovo | Get number of de novo signatures
get_n_groups | Get number of groups
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 counts.
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 signatures.
print.bascule_obj | Print for class "bascule_obj".
refine_denovo_signatures | De novo signatures refinement.
skin_fit | Skin cohort BASCULE fit
skin_metadata | Skin cohort metadata
synthetic_data | Analysis of a synthetic cohort
which_conda_env | Retrieve the name of the currently loaded environment.