NTW
This is the development version of NTW; for the stable release version, see NTW.
Predict gene network using an Ordinary Differential Equation (ODE) based method
DOI: 10.18129/B9.bioc.NTW
Bioconductor version: Development (3.24)
This package predicts the gene-gene interaction network and identifies the direct transcriptional targets of the perturbation using an ODE (Ordinary Differential Equation) based method.
Author: Wei Xiao, Yin Jin, Darong Lai, Xinyi Yang, Yuanhua Liu, Christine Nardini
Maintainer: Yuanhua Liu <liuyuanhua at picb.ac.cn>
citation("NTW")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("NTW")
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("NTW")| NTW vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Preprocessing, Software |
| Version | 1.63.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) (16 years) |
| License | GPL-2 |
| Depends | R (>= 2.3.0) |
| Imports | mvtnorm, stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| 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 | NTW_1.63.0.tar.gz |
| Windows Binary (x86_64) | NTW_1.63.0.zip |
| macOS Binary (big-sur-x86_64) | NTW_1.63.0.tgz |
| macOS Binary (sonoma-arm64) | NTW_1.63.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/NTW |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/NTW |
| Bioc Package Browser | https://code.bioconductor.org/browse/NTW/ |
| Package Short Url | https://bioconductor.org/packages/NTW/ |
| Package Downloads Report | Download Stats |