vissE
This is the development version of vissE; for the stable release version, see vissE.
Visualising Set Enrichment Analysis Results
Bioconductor version: Development (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:
Maintainer: Dharmesh D. Bhuva <bhuva.d at wehi.edu.au>
citation("vissE")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Network, NetworkEnrichment, Software |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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_1.15.0.tar.gz |
| Windows Binary (x86_64) | vissE_1.15.0.zip |
| macOS Binary (x86_64) | vissE_1.15.0.tgz |
| macOS Binary (arm64) | vissE_1.15.0.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 |