recipe bioconductor-nempi

Inferring unobserved perturbations from gene expression data

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-nempi/meta.yaml

Takes as input an incomplete perturbation profile and differential gene expression in log odds and infers unobserved perturbations and augments observed ones. The inference is done by iteratively inferring a network from the perturbations and inferring perturbations from the network. The network inference is done by Nested Effects Models.

package bioconductor-nempi

(downloads) docker_bioconductor-nempi

versions:

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

depends bioconductor-epinem:

>=1.26.0,<1.27.0

depends bioconductor-mnem:

>=1.18.0,<1.19.0

depends r-base:

>=4.3,<4.4.0a0

depends r-e1071:

depends r-matrixstats:

depends r-naturalsort:

depends r-nnet:

depends r-randomforest:

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-nempi

and update with::

   mamba update bioconductor-nempi

To create a new environment, run:

mamba create --name myenvname bioconductor-nempi

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-nempi:<tag>

(see `bioconductor-nempi/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-nempi/README.html)