ternarynet
This is the released version of ternarynet; for the devel version, see ternarynet.
Ternary Network Estimation
Bioconductor version: Release (3.23)
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")):
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")
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 | 1.56.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (14.5 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_1.56.0.tar.gz |
| Windows Binary (x86_64) | ternarynet_1.56.0.zip |
| macOS Binary (big-sur-x86_64) | ternarynet_1.56.0.tgz |
| macOS Binary (sonoma-arm64) | ternarynet_1.56.0.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 |