ternarynet
Ternary Network Estimation
Bioconductor version: 3.24 · Package version: 1.57.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ternarynet")Details
| Maintainer | McCall N. Matthew <mccallm@gmail.com> |
| Author | Matthew N. McCall <mccallm@gmail.com>, Anthony Almudevar <Anthony_Alumudevar@urmc.rochester.edu>, David Burton <David_Burton@urmc.rochester.edu>, Harry Stern <harry.stern@rochester.edu> |
| License | GPL (>= 2) |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, CellBiology, GraphAndNetwork, Network, Software |
| Package Short Url | https://bioconductor.org/packages/ternarynet/ |
Citation
From within R, enter citation("ternarynet"):
Matthew N. McCall, Anthony Almudevar, David Burton, Harry Stern. ternarynet: Ternary Network Estimation. doi:10.18129/B9.bioc.ternarynet, R package version 1.57.0, https://bioconductor.org/packages/ternarynet.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | ternarynet_1.57.0.tar.gz |
| Windows binary (x86_64) | ternarynet_1.57.0.zip |
| macOS binary (arm64) | ternarynet_1.57.0.tgz |
| macOS binary (x86_64) | ternarynet_1.57.0.tgz |
Dependencies
Depends: R (>= 4.0)
Imports: utils, igraph, methods, graphics, stats, BiocParallel
Suggests: testthat