recipe bioconductor-carnival

A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/CARNIVAL.html

License:

GPL-3

Recipe:

/bioconductor-carnival/meta.yaml

An upgraded causal reasoning tool from Melas et al in R with updated assignments of TFs' weights from PROGENy scores. Optimization parameters can be freely adjusted and multiple solutions can be obtained and aggregated.

package bioconductor-carnival

(downloads) docker_bioconductor-carnival

versions:

2.12.0-0,  2.10.0-0,  2.8.0-0,  2.4.0-0,  2.2.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-igraph:

depends r-lpsolve:

depends r-readr:

depends r-rjson:

depends r-rmarkdown:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

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-carnival

and update with::

   mamba update bioconductor-carnival

To create a new environment, run:

mamba create --name myenvname bioconductor-carnival

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-carnival:<tag>

(see `bioconductor-carnival/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an install-with-bioconda 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-carnival/README.html)