DO_similarity           Calculate Disease Ontology (DO) semantic
                        similarity matrix
GO_similarity           Calculate Gene Ontology (GO) semantic
                        similarity matrix
all_clustering_methods
                        All clustering methods
anno_word_cloud         Word cloud annotations
anno_word_cloud_from_GO
                        Word cloud annotations from GO
binary_cut              Cluster functional terms by recursively binary
                        cutting the similarity matrix
cluster_by_MCL          Cluster similarity matrix by MCL
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_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
count_word_from_GO      Calculate word frequency From GO
dend_node_apply         Apply functions on every node in a dendrogram
difference_score        Difference score
edit_node               Modify nodes in a dendrogram
export_to_shiny_app     Interactively visualize the similarity heatmap
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
simplifyGOFromMultipleLists
                        Perform simplifyGO analysis with multiple lists
                        of GO IDs
subset_enrichResult     Subset method of the enrichResult class
term_similarity         Similarity between terms based on the overlap
                        of genes
term_similarity_from_KEGG
                        Similarity between KEGG terms
term_similarity_from_MSigDB
                        Similarity between MSigDB terms
term_similarity_from_Reactome
                        Similarity between Reactome terms
term_similarity_from_enrichResult
                        Similarity between terms in the enrichResult
                        class
term_similarity_from_gmt
                        Similarity between terms from a gmt file
widthDetails.word_cloud
                        Width for word_cloud grob
word_cloud_grob         A simple grob for the word cloud
