recipe bioconductor-gemini

GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens

Homepage:

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

License:

BSD_3_clause + file LICENSE

Recipe:

/bioconductor-gemini/meta.yaml

GEMINI uses log-fold changes to model sample-dependent and independent effects, and uses a variational Bayes approach to infer these effects. The inferred effects are used to score and identify genetic interactions, such as lethality and recovery. More details can be found in Zamanighomi et al. 2019 (in press).

package bioconductor-gemini

(downloads) docker_bioconductor-gemini

versions:
1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0, 

1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-magrittr:

depends r-mixtools:

depends r-pbmcapply:

depends r-scales:

requirements:

additional platforms:

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-gemini

and update with::

   mamba update bioconductor-gemini

To create a new environment, run:

mamba create --name myenvname bioconductor-gemini

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-gemini:<tag>

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

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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-gemini/README.html)