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ternarynet

Ternary Network Estimation


Bioconductor version: Release (3.19)

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 (from within R, enter 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 PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, CellBiology, GraphAndNetwork, Network, Software
Version 1.48.0
In Bioconductor since BioC 2.10 (R-2.15) (12 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_1.48.0.tar.gz
Windows Binary ternarynet_1.48.0.zip (64-bit only)
macOS Binary (x86_64) ternarynet_1.48.0.tgz
macOS Binary (arm64) ternarynet_1.48.0.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