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Bioconductor - vissE

vissE

This is the released version of vissE; for the devel version, see vissE.

Visualising Set Enrichment Analysis Results

Bioconductor version: Release (3.21)

This package enables the interpretation and analysis of results from a gene set enrichment analysis using network-based and text-mining approaches. Most enrichment analyses result in large lists of significant gene sets that are difficult to interpret. Tools in this package help build a similarity-based network of significant gene sets from a gene set enrichment analysis that can then be investigated for their biological function using text-mining approaches.

Author: Dharmesh D. Bhuva [aut, cre] ORCID: 0000-0002-6398-9157 , Ahmed Mohamed [ctb]

Maintainer: Dharmesh D. Bhuva <bhuva.d at wehi.edu.au>

Citation (from within R, enter citation("vissE")): Installation

To install this package, start R (version "4.5") and enter:


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

BiocManager::install("vissE")

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("vissE")

Details biocViews GeneExpression, GeneSetEnrichment, Network, NetworkEnrichment, Software Version 1.16.0 In Bioconductor since BioC 3.13 (R-4.1) (4 years) License GPL-3 Depends R (>= 4.1) Imports igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm, ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb, ggrepel, textstem, tidygraph, stats, scales, ggraph System Requirements URL https://davislaboratory.github.io/vissE Bug Reports https://github.com/DavisLaboratory/vissE/issues See More Suggests testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr Linking To Enhances Depends On Me Imports Me Suggests Me msigdb Links To Me Build Report Build Report Package Archives

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

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