| all_clustering_methods | Configure clustering methods |
| anno_word_cloud | Word cloud annotations |
| anno_word_cloud_from_GO | Word cloud annotations from GO |
| area_above_ecdf | Area above the eCDF curve |
| binary_cut | Cluster functional terms by recursively binary cutting the similarity matrix |
| cluster_by_apcluster | Cluster terms based on their similarity matrix |
| cluster_by_dynamicTreeCut | Cluster terms based on their similarity matrix |
| cluster_by_fast_greedy | Cluster terms based on their similarity matrix |
| cluster_by_hdbscan | Cluster terms based on their similarity matrix |
| cluster_by_kmeans | Cluster terms based on their similarity matrix |
| cluster_by_leading_eigen | Cluster terms based on their similarity matrix |
| cluster_by_louvain | Cluster terms based on their similarity matrix |
| cluster_by_MCL | Cluster terms based on their similarity matrix |
| cluster_by_mclust | Cluster terms based on their similarity matrix |
| cluster_by_pam | Cluster terms based on their similarity matrix |
| cluster_by_walktrap | Cluster terms based on their similarity matrix |
| cluster_terms | Cluster terms based on their similarity matrix |
| cmp_make_clusters | Compare clustering methods |
| cmp_make_plot | Compare clustering methods |
| compare_clustering_methods | Compare clustering methods |
| count_words | Calculate word frequency |
| dend_node_apply | Apply functions on every node in a dendrogram |
| difference_score | Difference score |
| edit_node | Apply functions on every node in a dendrogram |
| export_to_shiny_app | Interactively visualize the similarity heatmap |
| GO_similarity | Calculate Gene Ontology (GO) semantic similarity matrix |
| guess_ont | Calculate Gene Ontology (GO) semantic similarity matrix |
| heightDetails.word_cloud | A simple grob for the word cloud |
| ht_clusters | Visualize the similarity matrix and the clustering |
| keyword_enrichment_from_GO | Keyword enrichment for GO terms |
| partition_by_hclust | Partition the matrix |
| partition_by_kmeans | Partition the matrix |
| partition_by_kmeanspp | Partition the matrix |
| partition_by_pam | Partition the matrix |
| plot_binary_cut | Cluster functional terms by recursively binary cutting the similarity matrix |
| random_GO | Calculate Gene Ontology (GO) semantic similarity matrix |
| register_clustering_methods | Configure clustering methods |
| remove_clustering_methods | Configure clustering methods |
| reset_clustering_methods | Configure clustering methods |
| scale_fontsize | Scale font size |
| select_cutoff | Select the cutoff for binary cut |
| se_opt | Global parameters |
| simplifyEnrichment | Simplify Gene Ontology (GO) enrichment results |
| simplifyGO | Simplify Gene Ontology (GO) enrichment results |
| simplifyGOFromMultipleLists | Perform simplifyGO analysis with multiple lists of GO IDs |
| summarizeGO | A simplified way to visualize enrichment in GO clusters |
| widthDetails.word_cloud | A simple grob for the word cloud |
| word_cloud_grob | A simple grob for the word cloud |