ViSEAGO

DOI: 10.18129/B9.bioc.ViSEAGO  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Annotation, Clustering, GO, GeneSetEnrichment, MultipleComparison, Software, Visualization
Version	1.12.0
In Bioconductor since	BioC 3.10 (R-3.6) (3.5 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
LinkingTo
Suggests	htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager
SystemRequirements
Enhances
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
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ViSEAGO_1.12.0.tar.gz
Windows Binary	ViSEAGO_1.12.0.zip
macOS Binary (x86_64)	ViSEAGO_1.12.0.tgz
macOS Binary (arm64)	ViSEAGO_1.12.0.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