Simplify Functional Enrichment Results


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Documentation for package ‘simplifyEnrichment’ version 2.2.0

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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