Simplify Functional Enrichment Results

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Documentation for package ‘simplifyEnrichment’ version 2.1.0

• 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