- recipe bioconductor-ternarynet
Ternary Network Estimation
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/ternarynet.html
- License:
GPL (>= 2)
- Recipe:
- Links:
biotools: ternarynet
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.
- package bioconductor-ternarynet¶
- versions:
1.46.0-0
,1.44.0-0
,1.42.0-1
,1.42.0-0
,1.38.0-2
,1.38.0-1
,1.38.0-0
,1.36.0-0
,1.34.0-1
,1.46.0-0
,1.44.0-0
,1.42.0-1
,1.42.0-0
,1.38.0-2
,1.38.0-1
,1.38.0-0
,1.36.0-0
,1.34.0-1
,1.34.0-0
,1.32.0-0
,1.30.0-0
,1.28.0-1
,1.28.0-0
,1.26.0-0
,1.24.0-0
,1.22.0-0
,1.20.0-0
- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0
- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0a0
- depends libblas:
>=3.9.0,<4.0a0
- depends libgcc-ng:
>=12
- depends liblapack:
>=3.9.0,<4.0a0
- depends libstdcxx-ng:
>=12
- depends r-base:
>=4.3,<4.4.0a0
- depends r-igraph:
- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-ternarynet and update with:: mamba update bioconductor-ternarynet
To create a new environment, run:
mamba create --name myenvname bioconductor-ternarynet
with
myenvname
being a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-ternarynet:<tag> (see `bioconductor-ternarynet/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ternarynet/README.html)