Simplify Functional Enrichment Results

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Documentation for package ‘simplifyEnrichment’ version 1.2.0

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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_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_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
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
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_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