Function reference • simplifyEnrichment

All functions
`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
`area_above_ecdf()`	Area above the eCDF curve
`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_by_pam()`	Cluster similarity matrix by pam clustering
`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_words()`	Calculate word frequency
`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
`keyword_enrichment_from_GO()`	Keyword enrichment for GO terms
`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
`se_opt()`	Global parameters
`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

Reference

All functions