recipe bioconductor-synaptome.data

AnnotationData for Synaptome.DB package

Homepage:

https://bioconductor.org/packages/3.18/data/annotation/html/synaptome.data.html

License:

Artistic-2.0

Recipe:

/bioconductor-synaptome.data/meta.yaml

The package provides access to the copy of the Synaptic proteome database. It was designed as an accompaniment for Synaptome.DB package. Database provides information for specific synaptic genes and allows building the protein-protein interaction graph for gene sets, synaptic compartments, and brain regions. In the current update we added 6 more synaptic proteome studies, which resulted in total of 64 studies. We introduced Synaptic Vesicle as a separate compartment. We also added coding mutations for Autistic Spectral disorder and Epilepsy collected from publicly available databases.

package bioconductor-synaptome.data

(downloads) docker_bioconductor-synaptome.data

versions:

0.99.6-2,  0.99.6-1,  0.99.6-0,  0.99.3-1,  0.99.3-0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-data-packages:

>=20231203

depends curl:

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-synaptome.data

and update with::

   mamba update bioconductor-synaptome.data

To create a new environment, run:

mamba create --name myenvname bioconductor-synaptome.data

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-synaptome.data:<tag>

(see `bioconductor-synaptome.data/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-synaptome.data/README.html)