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ViSEAGO

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


Bioconductor version: Release (3.18)

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.

Author: Aurelien Brionne [aut, cre], Amelie Juanchich [aut], Christelle hennequet-antier [aut]

Maintainer: Aurelien Brionne <aurelien.brionne at inrae.fr>

Citation (from within R, enter citation("ViSEAGO")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ViSEAGO")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ViSEAGO")
1: ViSEAGO HTML R Script
2: mouse_bionconductor HTML R Script
3: fgsea_alternative HTML R Script
4: SS_choice HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, Clustering, GO, GeneSetEnrichment, MultipleComparison, Software, Visualization
Version 1.16.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-3
Depends R (>= 3.6)
Imports data.table, AnnotationDbi, AnnotationForge, biomaRt, dendextend, DiagrammeR, DT, dynamicTreeCut, fgsea, GOSemSim, ggplot2, GO.db, grDevices, heatmaply, htmlwidgets, igraph, methods, plotly, processx, topGO, RColorBrewer, R.utils, scales, stats, UpSetR, utils
System Requirements
URL https://www.bioconductor.org/packages/release/bioc/html/ViSEAGO.html https://forgemia.inra.fr/UMR-BOA/ViSEAGO
Bug Reports https://forgemia.inra.fr/UMR-BOA/ViSEAGO/issues
See More
Suggests htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager
Linking To
Enhances
Depends On Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ViSEAGO_1.16.0.tar.gz
Windows Binary ViSEAGO_1.16.0.zip
macOS Binary (x86_64) ViSEAGO_1.16.0.tgz
macOS Binary (arm64) ViSEAGO_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ViSEAGO
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ViSEAGO
Bioc Package Browser https://code.bioconductor.org/browse/ViSEAGO/
Package Short Url https://bioconductor.org/packages/ViSEAGO/
Package Downloads Report Download Stats