recipe bioconductor-netactivity

Compute gene set scores from a deep learning framework

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-netactivity/meta.yaml

#' NetActivity enables to compute gene set scores from previously trained sparsely-connected autoencoders. The package contains a function to prepare the data (`prepareSummarizedExperiment`) and a function to compute the gene set scores (`computeGeneSetScores`). The package `NetActivityData` contains different pre-trained models to be directly applied to the data. Alternatively, the users might use the package to compute gene set scores using custom models.

package bioconductor-netactivity

versions:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-airway:

>=1.22.0,<1.23.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-delayedmatrixstats:

>=1.24.0,<1.25.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-netactivitydata:

>=1.4.0,<1.5.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

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-netactivity

and update with::

   mamba update bioconductor-netactivity

To create a new environment, run:

mamba create --name myenvname bioconductor-netactivity

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-netactivity:<tag>

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

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Link to this page

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