Man pages for vittoriofortino84/COPS
Clustering algorithms for Omics-driven Patient Stratification
| ad_ge_micro_zscore | Atopic dermatitis data |
| ad_studies | Atopic dermatitis studies |
| brca_multi_omics | Breast cancer multi-omic data |
| cbind_fill | Cbind modification which fills missing rows with NA using... |
| center_kernel | Kernel clustering utilities |
| cluster_associations | Association analysis for clustering results |
| clustering_analysis | Clustering, internal evaluation and batch effect estimation |
| clustering_dissimilarity_from_data | Dissimilarity matrix |
| clustering_metrics | Internal evaluation of clustering results |
| coexpression_network_unweighted | Unweighted gene co-expression network constructor |
| COPS | Clustering algorithms for Omics based Patient Stratification |
| data_preprocess | Data pre-processing for COPS pipelines |
| dimensionality_reduction | Dimensionality reduction suite |
| DSC | Dispersion Separability Criterion |
| ecdf_transform | Empirical cumulative density function transformation |
| ECMC | Enhanced consensus multi-view clustering |
| expressionToRWFeatures | Gene expression to gene seeds to RWR on PPI into FGSEA scores |
| feature_associations | Feature batch-effect analysis |
| format_scores | Renames internal method and score names to something more... |
| gene_module_eigengenes | Gene module eigen genes |
| gene_module_score | Gene module score |
| genes_to_pathways | Transform a gene-level data matrix into path-level... |
| getHumanPPIfromSTRINGdb | Retrieve human protein-protein interaction network from... |
| get_kernel_weights | Extract kernel weights from MKKM-MR clustering results |
| get_multi_omic_kernels | Multi-omic kernels |
| global_kernel_kmeans | Global kernel k-means (Tzortzis & Likas 2008) |
| heatmap_annotated | Annotated heatmap |
| heatmap_annotations | Heatmap annotation automation |
| jaccard_matrix | Jaccard index between indicator matrix columns |
| jaccard_similarity | Jaccard similarity coefficient between two partitions |
| KEGG_networks | Download KEGG pathway graphs |
| kernelized_kmeans | Kernelized k-means |
| kernel_kmeans | Kernel k-means |
| knn_g | Generate KNN graph from |
| mkkm_mr | Multiple kernel k-means with matrix induced regularization... |
| multi_omic_clustering | Multi-omic clustering via multi-view clustering or... |
| node_betweenness_parallel | Parallel computation of node betweenness |
| pareto_fronts | Pareto based multi-objective optimization |
| pareto_plot | Pairwise plots for visual Pareto based multi-objective... |
| pathway_gene_subnetworks | Extract subnetworks based on pathway genesets |
| pathway_networks | Pathway networks associated with cancer hallmarks |
| PIK | Pathway induced kernel (Manica et al. 2019) |
| plot_pvalues | Plot p-values in -log10 scale with original labels |
| plot_similarity_matrix | Plot similarity matrix as a heatmap |
| psoriasis_clinical_example | Psoriasis clinical data |
| psoriasis_degs_example | Psoriasis example genes |
| psoriasis_example_MEs | Meta-gene features for psoriasis expression data |
| psoriasis_rnaseq_corrected | Batch corrected psoriasis expression data |
| psoriasis_rnaseq_example | Psoriasis expression data |
| psoriasis_rnaseq_normalized | Normalized psoriasis expression data |
| rbind_fill | Rbind modification which fills missing columns with NA using... |
| reorder_method_factors | Reorder factors in scores to organize plots |
| retrieveDiseaseGenesOT | Retrieve disease-gene associations from the Open Targets... |
| RWRFGSEA | Random walk with restart and FGSEA |
| scoring | Scoring of dimensionality reduction and clustering pipeline... |
| seeded_rwr | Random walk with restart |
| stability_evaluation | Clustering stability evaluation |
| subsample_association_analysis | Cross-validated cluster association analysis |
| subsample_clustering_evaluation | Clustering analysis on cross-validated data sets |
| subsample_dimred | Dimensionality reduction on subsampled data sets |
| subsample_module_evaluation | Gene module correlation score for multiple clustering results |
| subsample_pathway_enrichment | Cross-validation wrapped pathway enrichment |
| subsample_survival_evaluation | Likelihood ratio analysis of Cox PH survival models for... |
| subsampling | Subsampling permutations of clustering dataset |
| survival_preprocess | Pre-process event data for survival analysis |
| triple_viz | Data visualization using PCA, t-SNE and UMAP |
| univariate_features | Univariate group difference tests for feature selection |
| unsigned_TOM_matrix | Topology overlap measure |
| weighted_linear_kernel | Weighted linear kernel |
