API for ddeweerd/MODifieRDev
MODifieRDev
| Global functions | |
|---|---|
| .onLoad | Source code |
| S2B | Man page Source code |
| S2B_core | Source code |
| add.vertex.attri | Source code |
| aggregate_colors | Source code |
| annotate_probe | Source code |
| build_clique_db | Man page Source code |
| calculate_correlation | Source code |
| check_diff_genes | Source code |
| check_expression_matrix | Source code |
| check_significance | Source code |
| clique_sum_core_exact | Source code |
| clique_sum_core_permutation | Source code |
| clique_sum_exact | Man page Source code |
| clique_sum_permutation | Man page Source code |
| collapse_probes | Source code |
| color_module_exact_test | Source code |
| compare_clique_scores | Source code |
| connect_db | Source code |
| construct_correlation_module | Source code |
| construct_diffcoex_module | Source code |
| construct_local_mod | Source code |
| construct_mcode_module | Source code |
| construct_module_set | Source code |
| construct_nlocal_mod | Source code |
| construction_mod | Source code |
| correlation_adjust_cutoff | Man page Source code |
| correlation_clique | Man page Source code |
| correlation_set_module_size | Man page Source code |
| count_matrix | Man page |
| create_clique_file | Source code |
| create_custom_microarray_input_object | Man page Source code |
| create_custom_rna_input_object | Man page Source code |
| create_fisher_tables | Source code |
| create_group_factor | Source code |
| create_input_microarray | Man page |
| create_input_rnaseq | Man page Source code |
| create_module_set | Man page Source code |
| dataframe_to_vector | Source code |
| diamond | Man page Source code |
| diamond_add_seed_genes | Man page Source code |
| diamond_remove_seed_genes | Man page Source code |
| diffcoex | Man page Source code |
| diffcoex_get_p_values | Source code |
| diffcoex_split_module_by_color | Man page Source code |
| differential_expression | Source code |
| entrez_to_index | Source code |
| entrez_to_symbol | Man page Source code |
| evaluate_table | Source code |
| export | Source code |
| export_xlsx | Source code |
| expression_matrix | Man page |
| extract_module_class | Source code |
| fisher_pval | Source code |
| get_chunk_table | Source code |
| get_chunk_table_perm | Source code |
| get_chunks | Source code |
| get_chunks_perm | Source code |
| get_clique_cutoffs | Source code |
| get_combinations | Source code |
| get_cutoffs | Source code |
| get_diffgene_cutoff | Source code |
| get_gene_frequencies | Source code |
| get_gene_presence | Source code |
| get_gene_table | Source code |
| get_intersections | Source code |
| get_max_frequency | Man page Source code |
| get_module_frame | Source code |
| get_module_genes | Source code |
| get_significant_rows | Source code |
| get_softthreshold_value | Source code |
| index_to_entrez | Source code |
| index_to_gene | Source code |
| infer_cliques | Source code |
| makes2btable | Source code |
| matrix_to_dataframe | Source code |
| mcode | Source code |
| mcode.find.complex | Source code |
| mcode.find.complexex | Source code |
| mcode.fluff.complex | Source code |
| mcode.post.process | Source code |
| mcode.vertex.weighting | Source code |
| mcode_adjust_score | Source code |
| mcode_split_modules | Source code |
| mod_mcode | Man page Source code |
| moda | Man page Source code |
| moda_change_specific_threshold | Man page Source code |
| moda_extract_modules_index_conserved | Source code |
| moda_extract_modules_index_specific | Source code |
| moduleDiscoverer.createDatabase | Source code |
| moduleDiscoverer.db.create_MD_object | Source code |
| moduleDiscoverer.db.extractEnrichedCliques | Source code |
| moduleDiscoverer.db.testForCliqueEnrichment | Source code |
| moduleDiscoverer.fragmentGraph | Source code |
| moduleDiscoverer.module.createModule | Source code |
| module_dispersion | Source code |
| module_to_igraph | Source code |
| modulediscoverer | Man page Source code |
| multineibstat2 | Source code |
| perform_iterations | Source code |
| permute_modules | Source code |
| permute_scores | Source code |
| plot.MODifieR_module | Source code |
| ppi_network | Man page |
| prepare_export | Source code |
| prepare_export.Clique_Sum_exact | Source code |
| prepare_export.Clique_Sum_permutation | Source code |
| prepare_export.Correlation_clique | Source code |
| prepare_export.DIAMOnD | Source code |
| prepare_export.DiffCoEx | Source code |
| prepare_export.MODA | Source code |
| prepare_export.MODifieR_input | Source code |
| prepare_export.Mcode | Source code |
| prepare_export.Module_set | Source code |
| prepare_export.S2B | Source code |
| prepare_export.WGCNA | Source code |
| prepare_export.module_discoverer | Source code |
| prepare_object | Source code |
| preprocess_object | Source code |
| probe_annotation | Man page |
| process_clique | Source code |
| recalculate_diff_genes | Man page Source code |
| recalculate_expression | Man page Source code |
| s2bthreshold | Source code |
| scale_observations | Source code |
| seedrows | Source code |
| settings_function | Source code |
| simpmain | Source code |
| subS2B | Source code |
| summarize_probes | Source code |
| summary.MODifieR_input | Source code |
| summary.MODifieR_module | Source code |
| symbol_to_entrez | Man page Source code |
| table_gene_by_method | Source code |
| validate_boolean | Source code |
| validate_diff_genes | Source code |
| validate_exprs_matrix | Source code |
| validate_indici | Source code |
| validate_inputs | Source code |
| validate_integer | Source code |
| validate_matrix | Source code |
| validate_new_input_objects | Source code |
| validate_numeric | Source code |
| validate_ppi | Source code |
| validate_unitinterval | Source code |
| wgcna | Man page Source code |
| wgcna_adjust_significance | Man page Source code |
| wgcna_get_all_module_genes | Man page Source code |
| wgcna_get_module_genes | Source code |
| wgcna_get_module_genes_by_sign | Man page Source code |
| wgcna_get_trait_data | Source code |
| wgcna_module_constructor | Source code |
| wgcna_set_module_size | Man page Source code |
| wgcna_split_module_by_color | Man page Source code |
| write_export | Source code |
