Simplify Functional Enrichment Results

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Documentation for package ‘simplifyEnrichment’ version 1.8.0

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

Help Pages

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_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_MCL	Cluster similarity matrix by MCL
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
DO_similarity	Calculate Disease Ontology (DO) semantic similarity matrix
edit_node	Modify nodes in a dendrogram
export_to_shiny_app	Interactively visualize the similarity heatmap
GO_similarity	Calculate Gene Ontology (GO) semantic similarity matrix
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
select_cutoff	Select the cutoff for binary cut
se_opt	Global parameters
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_enrichResult	Similarity between terms in the enrichResult class
term_similarity_from_gmt	Similarity between terms from a gmt file
term_similarity_from_KEGG	Similarity between KEGG terms
term_similarity_from_MSigDB	Similarity between MSigDB terms
term_similarity_from_Reactome	Similarity between Reactome terms
widthDetails.word_cloud	Width for word_cloud grob
word_cloud_grob	A simple grob for the word cloud