:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-nempi' .. highlight: bash bioconductor-nempi ================== .. conda:recipe:: bioconductor-nempi :replaces_section_title: :noindex: 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. .. conda:package:: bioconductor-nempi |downloads_bioconductor-nempi| |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: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `bioconductor-nempi/tags`_ for valid values for ````) .. |downloads_bioconductor-nempi| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-nempi.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-nempi :alt: (downloads) .. |docker_bioconductor-nempi| image:: https://quay.io/repository/biocontainers/bioconductor-nempi/status :target: https://quay.io/repository/biocontainers/bioconductor-nempi .. _`bioconductor-nempi/tags`: https://quay.io/repository/biocontainers/bioconductor-nempi?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html 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) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-nempi/README.html