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

annotate-methodsRetrieve GO annotations for a specie from genomic ressource...
available_organisms-methodsDisplay available organisms from a specified database.
Bioconductor2GOCheck available organisms databases at Bioconductor.
build_GO_SS-methodsbuild GO Semantic Similarity object.
clusters_cor-methodsCompute distance matrix between dendrograms partitions.
compare_clusters-methodsHeatmap to compare partitions
compute_SS_distances-methodsCompute distance between GO terms or GO clusters based on...
create_topGOdata-methodsCreate topGOdata object for enrichment test with topGO...
Custom2GOStore organisms GO annotations from custom database file.
enrich_GO_terms-classenrich_GO_terms class object definition.
Ensembl2GOCheck available organisms datasets at Ensembl.
EntrezGene2GOStore available organisms GO annotations at EntrezGene.
EntrezGene_orthologsDownload EntrezGene orthologs groups.
fgsea-classfgsea class object definition.
gene2GO-classgene2GO class object definition.
genomic_ressource-classgenomic_ressource class object definition.
GO_clusters-classGO_clusters class object
GOclusters_heatmap-methodsBuild a clustering heatmap on GO groups.
GOcount-methodsBarplot for the count of GO terms.
GO_SS-classGO_SS class object definition.
GOterms_heatmap-methodsBuild a clustering heatmap on GO terms.
MDSplot-methodsMulti Dimensional Scale (MDS) plot
merge_enrich_terms-methodsMerge enriched GO terms.
myGOsmyGOs dataset
overLapperbuild all sets combinations intersections
pkgdiagramDisplay the ViSEAGO package diagram.
runfgsea-methodsperform multilevel preranked gene set enrichment analysis.
show_heatmap-methodsDisplay an interactive or static heatmap.
show_table-methodsDisplay an interactive or static table.
taxonomyDisplay Organism Scientific and common name from taxid.
Uniprot2GOCheck available organisms databases at Uniprot.
Upset-methodsEnriched GO terms intersections plot.
ViSEAGO documentation built on Nov. 8, 2020, 6:51 p.m.