GNET2
This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see GNET2.
Constructing gene regulatory networks from expression data through functional module inference
Bioconductor version: Release (3.23)
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")):
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("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 | 1.27.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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_1.27.0.tar.gz |
| Windows Binary (x86_64) | GNET2_1.27.0.zip |
| macOS Binary (big-sur-x86_64) | GNET2_1.27.0.tgz |
| macOS Binary (sonoma-arm64) | GNET2_1.27.0.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 |