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vissE

Visualising Set Enrichment Analysis Results


Bioconductor version: Release (3.18)

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] , 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 "4.3") 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")
vissE HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, GeneSetEnrichment, Network, NetworkEnrichment, Software
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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.

Source Package vissE_1.10.0.tar.gz
Windows Binary vissE_1.10.0.zip
macOS Binary (x86_64) vissE_1.10.0.tgz
macOS Binary (arm64) vissE_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/vissE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/vissE
Bioc Package Browser https://code.bioconductor.org/browse/vissE/
Package Short Url https://bioconductor.org/packages/vissE/
Package Downloads Report Download Stats