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| all_clustering_methods | All clustering methods |
| binary_cut | Cluster functional terms by recursively binary cutting the similarity matrix |
| cluster_by_apcluster | Cluster similarity matrix by apcluster |
| cluster_by_dynamicTreeCut | Cluster similarity matrix by dynamicTreeCut |
| cluster_by_hdbscan | Cluster similarity matrix by hdbscan |
| cluster_by_igraph | Cluster similarity matrix by graph community detection methods |
| cluster_by_kmeans | Cluster similarity matrix by k-means clustering |
| cluster_by_MCL | Cluster similarity matrix by MCL |
| cluster_by_mclust | Cluster similarity matrix by mclust |
| cluster_terms | Cluster functional terms |
| cmp_make_clusters | Apply various clustering methods |
| cmp_make_plot | Make plots for comparing clustering methods |
| compare_clustering_methods | Compare clustering methods |
| count_word | Calculate word frequency |
| dend_node_apply | Apply functions on every node in a dendrogram |
| difference_score | Difference score |
| DO_similarity | Calculate Disease Ontology (DO) semantic similarity matrix |
| edit_node | Modify nodes in a dendrogram |
| GO_similarity | Calculate Gene Ontology (GO) semantic similarity matrix |
| guess_ont | Guess the ontology of the input GO IDs |
| heightDetails.word_cloud | Height for word_cloud grob |
| ht_clusters | Visualize the similarity matrix and the clustering |
| partition_by_hclust | Partition by hclust |
| partition_by_kmeans | Partition by kmeans |
| partition_by_kmeanspp | Partition by kmeans++ |
| partition_by_pam | Partition by PAM |
| plot_binary_cut | Visualize the process of binary cut |
| random_DO | Generate random Disease Ontology (DO) IDs |
| random_GO | Generate random GO IDs |
| register_clustering_methods | Register new clustering methods |
| remove_clustering_methods | Remove clustering methods |
| reset_clustering_methods | Reset to default clustering methods |
| scale_fontsize | Scale font size |
| select_cutoff | Select the cutoff for binary cut |
| simplifyEnrichment | Simplify functional enrichment results |
| simplifyGO | Simplify Gene Ontology (GO) enrichment results |
| subset_enrichResult | Subset method of the enrichResult class |
| term_similarity | Similarity between terms based on the overlap of genes |
| term_similarity_from_enrichResult | Similarity between terms in the enrichResult class |
| term_similarity_from_gmt | Similarity between terms from a gmt file |
| term_similarity_from_KEGG | Similarity between KEGG terms |
| term_similarity_from_MSigDB | Similarity between MSigDB terms |
| term_similarity_from_Reactome | Similarity between Reactome terms |
| widthDetails.word_cloud | Width for word_cloud grob |
| word_cloud_grob | A simple grob for the word cloud |