gsean
This is the development version of gsean; for the stable release version, see gsean.
Gene Set Enrichment Analysis with Networks
Bioconductor version: Development (3.24)
Biological molecules in a living organism seldom work individually. They usually interact each other in a cooperative way. Biological process is too complicated to understand without considering such interactions. Thus, network-based procedures can be seen as powerful methods for studying complex process. However, many methods are devised for analyzing individual genes. It is said that techniques based on biological networks such as gene co-expression are more precise ways to represent information than those using lists of genes only. This package is aimed to integrate the gene expression and biological network. A biological network is constructed from gene expression data and it is used for Gene Set Enrichment Analysis.
Author: Dongmin Jung
Maintainer: Dongmin Jung <dmdmjung at gmail.com>
citation("gsean")):Dongmin Jung. gsean: Gene Set Enrichment Analysis with Networks. doi:10.18129/B9.bioc.gsean, R package version 1.33.0, https://bioconductor.org/packages/gsean.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("gsean")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("gsean")| gsean | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Network, NetworkEnrichment, Pathways, Software, StatisticalMethod |
| Version | 1.33.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5), fgsea, PPInfer |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi, knitr, plotly, WGCNA, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | gsean_1.33.0.tar.gz |
| Windows Binary (x86_64) | gsean_1.33.0.zip |
| macOS Binary (big-sur-x86_64) | gsean_1.33.0.tgz |
| macOS Binary (sonoma-arm64) | gsean_1.33.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/gsean |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/gsean |
| Package Short Url | https://bioconductor.org/packages/gsean/ |
| Package Downloads Report | Download Stats |