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

## Documentation for package ‘ViSEAGO’ version 1.4.0

- 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