ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

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Documentation for package ‘ViSEAGO’ version 1.6.0

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annotate Retrieve GO annotations for a specie from genomic ressource database.
annotate-method Retrieve GO annotations for a specie from genomic ressource database.
available_organisms Display available organisms from a specified database.
available_organisms-method Display available organisms from a specified database.
Bioconductor2GO Check available organisms databases at Bioconductor.
build_GO_SS build GO Semantic Similarity object.
build_GO_SS-method build GO Semantic Similarity object.
clusters_cor Compute distance matrix between dendrograms partitions.
clusters_cor-method Compute distance matrix between dendrograms partitions.
compare_clusters Heatmap to compare partitions
compare_clusters-method Heatmap to compare partitions
compute_SS_distances Compute distance between GO terms or GO clusters based on semantic similarity.
compute_SS_distances-method Compute distance between GO terms or GO clusters based on semantic similarity.
create_topGOdata Create topGOdata object for enrichment test with topGO package.
create_topGOdata-method Create topGOdata object for enrichment test with topGO package.
Custom2GO Store organisms GO annotations from custom database file.
enrich_GO_terms-class enrich_GO_terms class object definition.
Ensembl2GO Check available organisms datasets at Ensembl.
EntrezGene2GO Store available organisms GO annotations at EntrezGene.
fgsea-class fgsea class object definition.
gene2GO-class gene2GO class object definition.
genomic_ressource-class genomic_ressource class object definition.
GOclusters_heatmap Build a clustering heatmap on GO groups.
GOclusters_heatmap-method Build a clustering heatmap on GO groups.
GOcount Barplot for the count of GO terms.
GOcount-method Barplot for the count of GO terms.
GOterms_heatmap Build a clustering heatmap on GO terms.
GOterms_heatmap-method Build a clustering heatmap on GO terms.
GO_clusters-class GO_clusters class object
GO_SS-class GO_SS class object definition.
MDSplot Multi Dimensional Scale (MDS) plot
MDSplot-method Multi Dimensional Scale (MDS) plot
merge_enrich_terms Merge enriched GO terms.
merge_enrich_terms-method Merge enriched GO terms.
myGOs myGOs dataset
runfgsea perform multilevel preranked gene set enrichment analysis.
runfgsea-method perform multilevel preranked gene set enrichment analysis.
show_heatmap Display an interactive or static heatmap.
show_heatmap-method Display an interactive or static heatmap.
show_table Display an interactive or static table.
show_table-method Display an interactive or static table.
Uniprot2GO Check available organisms databases at Uniprot.
Upset Enriched GO terms intersections plot.
Upset-method Enriched GO terms intersections plot.
ViSEAGO ViSEAGO package