GNET2
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see GNET2.
Constructing gene regulatory networks from expression data through functional module inference
Bioconductor version: 3.12
Cluster genes to functional groups with E-M process. Iteratively perform TF assigning and Gene assigning, until the assignment of genes did not change, or max number of iterations is reached.
Author: Chen Chen, Jie Hou and Jianlin Cheng
Maintainer: Chen Chen <ccm3x at mail.missouri.edu>
citation("GNET2")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GNET2")
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("GNET2")| Build functional gene modules with GNET2 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Network, NetworkInference, Regression, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| License | Apache License 2.0 |
| Depends | R (>= 3.6) |
| Imports | ggplot2, xgboost, Rcpp, reshape2, grid, DiagrammeR, methods, stats, matrixStats, graphics, SummarizedExperiment, dplyr, igraph, grDevices, utils |
| System Requirements | |
| URL | https://github.com/chrischen1/GNET2 |
| Bug Reports | https://github.com/chrischen1/GNET2/issues |
See More
| Suggests | knitr, rmarkdown |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GNET2_1.6.0.tar.gz |
| Windows Binary | GNET2_1.6.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | GNET2_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GNET2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GNET2 |
| Bioc Package Browser | https://code.bioconductor.org/browse/GNET2/ |
| Package Short Url | https://bioconductor.org/packages/GNET2/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |