ternarynet
Ternary Network Estimation
Bioconductor version: Release (3.20)
Gene-regulatory network (GRN) modeling seeks to infer dependencies between genes and thereby provide insight into the regulatory relationships that exist within a cell. This package provides a computational Bayesian approach to GRN estimation from perturbation experiments using a ternary network model, in which gene expression is discretized into one of 3 states: up, unchanged, or down). The ternarynet package includes a parallel implementation of the replica exchange Monte Carlo algorithm for fitting network models, using MPI.
Author: Matthew N. McCall <mccallm at gmail.com>, Anthony Almudevar <Anthony_Alumudevar at urmc.rochester.edu>, David Burton <David_Burton at urmc.rochester.edu>, Harry Stern <harry.stern at rochester.edu>
Maintainer: McCall N. Matthew <mccallm at gmail.com>
citation("ternarynet")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ternarynet")
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("ternarynet")
ternarynet: A Computational Bayesian Approach to Ternary Network Estimation | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Bayesian, CellBiology, GraphAndNetwork, Network, Software |
Version | 1.50.0 |
In Bioconductor since | BioC 2.10 (R-2.15) (12.5 years) |
License | GPL (>= 2) |
Depends | R (>= 4.0) |
Imports | utils, igraph, methods, graphics, stats, BiocParallel |
System Requirements | |
URL |
See More
Suggests | testthat |
Linking To | |
Enhances | Rmpi, snow |
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 | ternarynet_1.50.0.tar.gz |
Windows Binary (x86_64) | ternarynet_1.50.0.zip |
macOS Binary (x86_64) | ternarynet_1.50.0.tgz |
macOS Binary (arm64) | ternarynet_1.50.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/ternarynet |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ternarynet |
Bioc Package Browser | https://code.bioconductor.org/browse/ternarynet/ |
Package Short Url | https://bioconductor.org/packages/ternarynet/ |
Package Downloads Report | Download Stats |