recipe bioconductor-attract

Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

Homepage:

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

License:

LGPL (>= 2.0)

Recipe:

/bioconductor-attract/meta.yaml

This package contains the functions to find the gene expression modules that represent the drivers of Kauffman's attractor landscape. The modules are the core attractor pathways that discriminate between different cell types of groups of interest. Each pathway has a set of synexpression groups, which show transcriptionally-coordinated changes in gene expression.

package bioconductor-attract

versions:

1.54.0-0,  1.52.0-0,  1.50.0-0,  1.46.0-0,  1.44.0-0,  1.42.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-0, 

1.54.0-0,  1.52.0-0,  1.50.0-0,  1.46.0-0,  1.44.0-0,  1.42.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.34.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-gostats:

>=2.68.0,<2.69.0

depends bioconductor-keggrest:

>=1.42.0,<1.43.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-org.hs.eg.db:

>=3.18.0,<3.19.0

depends bioconductor-reactome.db:

>=1.86.0,<1.87.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cluster:

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-attract

and update with::

   mamba update bioconductor-attract

To create a new environment, run:

mamba create --name myenvname bioconductor-attract

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-attract:<tag>

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

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