Package Recipe 'bioconductor-bnem'

recipe bioconductor-bnem

Training of logical models from indirect measurements of perturbation experiments

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/bnem.html
License:: GPL-3
Recipe:: /bioconductor-bnem/meta.yaml

bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of CellNOptR. Perturbation experiments of signalling nodes in cells are analysed for their effect on the global gene expression profile. Those profiles give evidence for the Boolean regulation of down-stream nodes in the network, e.g., whether two parents activate their child independently (OR-gate) or jointly (AND-gate).

package bioconductor-bnem¶

Versions:

1.18.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-affy >=1.88.0,<1.89.0
on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-cellnoptr >=1.56.0,<1.57.0
on bioconductor-epinem >=1.34.0,<1.35.0
on bioconductor-graph >=1.88.0,<1.89.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-mnem >=1.26.0,<1.27.0
on bioconductor-rgraphviz >=2.54.0,<2.55.0
on bioconductor-sva >=3.58.0,<3.59.0
on bioconductor-vsn >=3.78.0,<3.79.0
on r-base >=4.5,<4.6.0a0
on r-binom
on r-cluster
on r-flexclust
on r-matrixstats
on r-rcolorbrewer
on r-rmarkdown
on r-snowfall

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-bnem

to add into an existing workspace instead, run:

pixi add bioconductor-bnem

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-bnem

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-bnem

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-bnem:<tag>

(see bioconductor-bnem/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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-bnem/README.html)