vissE

DOI: 10.18129/B9.bioc.vissE  

Visualising Set Enrichment Analysis Results

Bioconductor version: Release (3.16)

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>

Installation

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

 

HTML	R Script	vissE
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GeneSetEnrichment, Network, NetworkEnrichment, Software
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 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
LinkingTo
Suggests	testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr
SystemRequirements
Enhances
URL	https://davislaboratory.github.io/vissE
BugReports	https://github.com/DavisLaboratory/vissE/issues
Depends On Me
Imports Me
Suggests Me	msigdb
Links To Me
Build Report

Package Archives

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

Source Package	vissE_1.6.0.tar.gz
Windows Binary	vissE_1.6.0.zip
macOS Binary (x86_64)	vissE_1.6.0.tgz
macOS Binary (arm64)	vissE_1.6.0.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