Package index
-
fit()
- Fit a bascule object
-
fit_clustering()
- Fit clustering
-
refine_denovo_signatures()
- De novo signatures refinement.
-
merge_clusters()
- Function to merge similar clusters
-
get_input()
- Get input data
-
get_signames()
- Get signatures names
-
get_fixed_signames()
- Get reference signatures names
-
get_denovo_signames()
- Get denovo signatures names
-
get_signatures()
- Get signatures
-
get_fixed_signatures()
- Get fixed (reference) signatures
-
get_denovo_signatures()
- Get de novo (reference) signatures
-
get_exposure()
- Get exposures
-
convert_dn_names()
- Function to map de novo signatures to input catalogues
-
plot_data()
- Function to visualize the input and reconstructed mutation counts.
-
plot_signatures()
- Function to visualize the estimated and reference signatures.
-
plot_exposures()
- Function to visualize the estimated exposures
-
plot_centroids()
- Plot clustering centroids
-
plot_fit()
- Report of the fit
-
plot_similarity_reference()
- Function to visualize the similarity of denovo and reference signatures.
-
plot_scores()
- Plot model selection scores
-
plot_gradient_norms()
- Plot parameters gradients norms
-
plot_posterior_probs()
- Plot posterior probabilities
-
print(<bascule_obj>)
- Print for class
'bascule_obj'
.
-
plot(<bascule_obj>)
- Plot for class
'bascule_obj'
.
-
COSMIC_sbs
- COSMIC catalogue for SBS (version 3.4, GRCh37)
-
COSMIC_sbs_filt
- COSMIC catalogue for SBS filtered (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_cn
- COSMIC catalogue for CN (version 3.4, GRCh37)
-
Degasperi_SBS
- Degasperi SBS catalogue
-
Degasperi_DBS
- Degasperi DBS catalogue
-
synthetic_data
- Analysis of a synthetic cohort
-
breast_data
- Analysis of breast tumours
-
configure_environment()
- Configure the reticulate environment
-
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.
-
which_conda_env()
- Retrieve the name of the currently loaded environment.