# Simplify Functional Enrichment Results

## Documentation for package ‘simplifyEnrichment’ version 2.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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