{ "_id": "6a197f44acfb0bcc41df7eaa", "Package": "ViSEAGO", "Version": "1.27.0", "Title": "ViSEAGO: a Bioconductor package for clustering biological\nfunctions using Gene Ontology and semantic similarity", "Author": "Aurelien Brionne [aut, cre], Amelie Juanchich [aut], Christelle\nhennequet-antier [aut]", "Maintainer": "Aurelien Brionne ", "Encoding": "UTF-8", "Description": "The main objective of ViSEAGO package is to carry out a\ndata mining of biological functions and establish links between\ngenes involved in the study. We developed ViSEAGO in R to\nfacilitate functional Gene Ontology (GO) analysis of complex\nexperimental design with multiple comparisons of interest. It\nallows to study large-scale datasets together and visualize GO\nprofiles to capture biological knowledge. The acronym stands\nfor three major concepts of the analysis: Visualization,\nSemantic similarity and Enrichment Analysis of Gene Ontology.\nIt provides access to the last current GO annotations, which\nare retrieved from one of NCBI EntrezGene, Ensembl or Uniprot\ndatabases for several species. Using available R packages and\nnovel developments, ViSEAGO extends classical functional GO\nanalysis to focus on functional coherence by aggregating\nclosely related biological themes while studying multiple\ndatasets at once. It provides both a synthetic and detailed\nview using interactive functionalities respecting the GO graph\nstructure and ensuring functional coherence supplied by\nsemantic similarity. ViSEAGO has been successfully applied on\nseveral datasets from different species with a variety of\nbiological questions. Results can be easily shared between\nbioinformaticians and biologists, enhancing reporting\ncapabilities while maintaining reproducibility.", "VignetteBuilder": "knitr", "License": "GPL-3", "URL": "https://www.bioconductor.org/packages/release/bioc/html/ViSEAGO.html,\nhttps://forgemia.inra.fr/UMR-BOA/ViSEAGO", "BugReports": "https://forgemia.inra.fr/UMR-BOA/ViSEAGO/issues", "biocViews": "Software, Annotation, GO, GeneSetEnrichment,\nMultipleComparison, Clustering, Visualization", "RoxygenNote": "7.3.2", "Collate": "'genomic_ressource.R' 'Bioconductor2GO.R' 'Ensembl2GO.R'\n'EntrezGene2GO.R' 'EntrezGene_orthologs.R' 'enrich_GO_terms.R'\n'GO_SS.R' 'GO_clusters.R' 'GOclusters_heatmap.R' 'GOcount.R'\n'GOterms_heatmap.R' 'MDSplot.R' 'Uniprot2GO.R' 'Upset.R'\n'ViSEAGO.R' 'annotate.R' 'available_organisms.R' 'gene2GO.R'\n'build_GO_SS.R' 'clusters_cor.R' 'compare_clusters.R'\n'compute_SS_distances.R' 'create_topGOdata.R' 'custom2GO.R'\n'datasets.R' 'fgsea.R' 'merge_enrich_terms.R' 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