adjusted_rand_index | Adjusted rand index |
analyze_survival | Plots the survival curves and compute the Cox p-value |
breast_cancer_data | Breast cancer multi-omics data |
check_distribution | Plot the distribution of the features |
consensus_spectral_clustering | Apply consensus clustering on affinity matrix. |
dunn_index | Dunn index |
entropy | Return entropy of vector |
evaluation | Evaluate parameters |
flag_data | Simple quality control on sample-feature matrices |
gbm_data | Glioblastoma multiforme (GBM) multi-omics data |
generate_multi_moclust | Generate simulated data |
generate_multi_structured | Generate synthetic data based on a list of features matrics. |
generate_multi_unstructured | Generate a list of synthetic data matrices for validation |
generate_partitions | Generate a partitions matrix |
generate_single_moclust | Generate simulated data |
generate_synth_data | Generate 'multi-omic' synthetic data matrices for validation |
get_method | Load built-in methods |
get_metric | Load built-in metrics |
hello | Hello, World! |
homogeneity_completeness_vmeasure | Homogeneity, completeness and V-Measure metrics for partition... |
meila_vi | Meila's variation of information index |
metrics_list | Metrics implemented |
mutual_information | Calculate mutual information of two vectors |
normalized_mutual_information | Normalized mutual information |
overview_metrics | An overview of the results with all available metrics |
plot_affinity_matrix | Plot clustered affinity matrix |
plot_clinical_features | Box-plot of clinical features for a given partition of the... |
pre_process | Pre-process feature matrices before analysis. |
select_features | Selection of important features |
select_mad | Mean Absolute Deviation (MAD) cutoff |
select_pca | Apply principal components analysis |
select_variance | Variance cutoff |
silhouette_affinity | Silhouette index for affinity matrix |
silhouette_distance | Classic silhouette index for distance matrix |
sparse_methylation | Sparse data to test tools |
subtype_anf | Subtypes using Affinity Network Fusion |
subtype_pins | Subtypes using PINSPlus package |
subtype_snf | Subtypes patients using Similarity Network Fusion |
tuning | Tunes the methods to have the best set of parameters |
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