vissE
This is the released version of vissE; for the devel version, see vissE.
Visualising Set Enrichment Analysis Results
Bioconductor version: Release (3.23)
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("vissE")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Network, NetworkEnrichment, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (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_1.20.0.tar.gz |
| Windows Binary (x86_64) | vissE_1.20.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | vissE_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | vissE_1.20.0.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 |