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 (64-bit only) |
| macOS Binary (x86_64) | ternarynet_1.50.0.tgz |
| macOS Binary (arm64) | ternarynet_1.49.0.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 |