Man pages for EGAD
Extending guilt by association by degree
| assortativity | Calculating network assortativity |
| atrr.human | Human GENCODE annotations (v22) |
| attr.mouse | Mouse GENCODE annotations (M7) |
| auc_multifunc | Calculating AUC for functional groups from ranked lists |
| auprc | Area under the precision recall curve |
| auroc_analytic | Area under the receiver operating characteristic curve |
| biogrid | BIOGRID v3.4.126 |
| build_binary_network | Builds a binary network |
| build_coexp_expressionSet | Builds a coexpression network from an expressionSet |
| build_coexp_GEOID | Builds a coexpression network given a GEO ID |
| build_coexp_network | Builds a coexpression network from an expressionSet |
| build_semantic_similarity_network | Builds a semantic similarity network |
| build_weighted_network | Builds a weighted network |
| calculate_multifunc | Performing multifunctionality analysis |
| conv_smoother | Plot smoothed curve |
| example_annotations | Example of annotations |
| example_binary_network | Example of binary network |
| example_coexpression | Example of binary network |
| example_neighbor_voting | Example of binary network |
| extend_network | Builds an extended network from a binary network |
| filter_network | Filter on matrix |
| filter_network_cols | Filter on columns |
| filter_network_rows | Filter on rows |
| filter_orthologs | Filter on orthologs |
| fmeasure | Fmeasure of precision-recall |
| genes | Genes from BIOGRID v3.4.126 |
| get_auc | Calculates the area under a curve |
| get_biogrid | Downloading and filtering BIOGRID |
| get_counts | Get counts |
| get_density | Get density |
| get_expression_data_gemma | Obtain expression matrix from the GEMMA database |
| get_expression_matrix_from_GEO | Obtain expression matrix from GEO database |
| get_phenocarta | Downloading and filtering Phenocarta |
| get_prc | Build precision-recall curve |
| get_roc | Build receiver operating characteristic curve |
| GO.human | GO - human |
| GO.mouse | GO - mouse |
| GO.voc | Gene ontology vocabulary |
| make_annotations | Creating gene annotations |
| make_genelist | Creating list of all genes in the data set. |
| make_gene_network | Creating gene-by-gene network |
| make_transparent | Make a color transparent (Taken from an answer on... |
| neighbor_voting | Evaluating Gene Function Prediction |
| node_degree | Calculate node degree |
| ortho | Gene orthologs |
| pheno | Phenocarta |
| plot_densities | Plot densities |
| plot_density_compare | Plot density comparisons |
| plot_distribution | Plot distribution histogram |
| plot_network_heatmap | Plot network heatmap |
| plot_prc | Plot precision recall curve |
| plot_roc | Plot receiver operating characteristic curve |
| plot_roc_overlay | Plot ROC overlay |
| plot_value_compare | Plot value comparisons |
| predictions | Performing Gene Function Prediction |
| repmat | Rep function for matrices |
| run_GBA | Performing 'Guilt by Association' Analysis |
