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

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Documentation for package ‘ViSEAGO’ version 1.18.0

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

Help Pages

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