Package: ViSEAGO
Version: 1.24.0
Title: ViSEAGO: a Bioconductor package for clustering biological
        functions using Gene Ontology and semantic similarity
Author: Aurelien Brionne [aut, cre], Amelie Juanchich [aut], Christelle
        hennequet-antier [aut]
Maintainer: Aurelien Brionne <aurelien.brionne@inrae.fr>
Imports: data.table, AnnotationDbi, dendextend, dynamicTreeCut,
        GOSemSim, GO.db, heatmaply, topGO, AnnotationForge, DT,
        DiagrammeR, R.utils, RColorBrewer, UpSetR, biomaRt, fgsea,
        ggplot2, htmlwidgets, igraph, methods, plotly, scales,
        ComplexHeatmap, circlize
Depends: R (>= 3.6)
Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr,
        rmarkdown, corrplot, remotes, BiocManager, stats, utils,
        grDevices, processx
Encoding: UTF-8
Description: The main objective of ViSEAGO package is to carry out a
        data mining of biological functions and establish links between
        genes involved in the study. We developed ViSEAGO in R to
        facilitate functional Gene Ontology (GO) analysis of complex
        experimental design with multiple comparisons of interest. It
        allows to study large-scale datasets together and visualize GO
        profiles to capture biological knowledge. The acronym stands
        for three major concepts of the analysis: Visualization,
        Semantic similarity and Enrichment Analysis of Gene Ontology.
        It provides access to the last current GO annotations, which
        are retrieved from one of NCBI EntrezGene, Ensembl or Uniprot
        databases for several species. Using available R packages and
        novel developments, ViSEAGO extends classical functional GO
        analysis to focus on functional coherence by aggregating
        closely related biological themes while studying multiple
        datasets at once. It provides both a synthetic and detailed
        view using interactive functionalities respecting the GO graph
        structure and ensuring functional coherence supplied by
        semantic similarity. ViSEAGO has been successfully applied on
        several datasets from different species with a variety of
        biological questions. Results can be easily shared between
        bioinformaticians and biologists, enhancing reporting
        capabilities while maintaining reproducibility.
VignetteBuilder: knitr
License: GPL-3
URL:
        https://www.bioconductor.org/packages/release/bioc/html/ViSEAGO.html,
        https://forgemia.inra.fr/UMR-BOA/ViSEAGO
BugReports: https://forgemia.inra.fr/UMR-BOA/ViSEAGO/issues
biocViews: Software, Annotation, GO, GeneSetEnrichment,
        MultipleComparison, Clustering, Visualization
RoxygenNote: 7.3.2
Collate: 'genomic_ressource.R' 'Bioconductor2GO.R' 'Ensembl2GO.R'
        'EntrezGene2GO.R' 'EntrezGene_orthologs.R' 'enrich_GO_terms.R'
        'GO_SS.R' 'GO_clusters.R' 'GOclusters_heatmap.R' 'GOcount.R'
        'GOterms_heatmap.R' 'MDSplot.R' 'Uniprot2GO.R' 'Upset.R'
        'ViSEAGO.R' 'annotate.R' 'available_organisms.R' 'gene2GO.R'
        'build_GO_SS.R' 'clusters_cor.R' 'compare_clusters.R'
        'compute_SS_distances.R' 'create_topGOdata.R' 'custom2GO.R'
        'datasets.R' 'fgsea.R' 'merge_enrich_terms.R' 'overlapper.R'
        'pkgdiagram.R' 'runfgsea.R' 'show_heatmap.R' 'show_table.R'
        'taxonomy.R'
Config/pak/sysreqs: libglpk-dev make libmagick++-dev gsfonts libicu-dev
        libpng-dev libxml2-dev libssl-dev perl libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:53:03 UTC
RemoteUrl: https://github.com/bioc/ViSEAGO
RemoteRef: RELEASE_3_22
RemoteSha: 9020dee04b152f3db33d14aaea20427bdfef5ce9
NeedsCompilation: no
Packaged: 2026-02-20 06:06:46 UTC; root
Built: R 4.5.2; ; 2026-02-20 06:09:37 UTC; windows
