recipe bioconductor-sbgnview.data

Supporting datasets for SBGNview package

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/SBGNview.data.html

License:

AGPL-3

Recipe:

/bioconductor-sbgnview.data/meta.yaml

This package contains: 1. A microarray gene expression dataset from a human breast cancer study. 2. A RNA-Seq gene expression dataset from a mouse study on IFNG knockout. 3. ID mapping tables between gene IDs and SBGN-ML file glyph IDs. 4. Percent of orthologs detected in other species of the genes in a pathway. Cutoffs of this percentage for defining if a pathway exists in another species. 5. XML text of SBGN-ML files for all pre-collected pathways.

package bioconductor-sbgnview.data

(downloads) docker_bioconductor-sbgnview.data

versions:
1.16.0-0,  1.14.0-0,  1.12.0-0,  1.11.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.1-0,  1.4.0-0, 

1.16.0-0,  1.14.0-0,  1.12.0-0,  1.11.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.1-0,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-data-packages:

>=20231203

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-bookdown:

depends r-knitr:

depends r-rmarkdown:

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-sbgnview.data

and update with::

   mamba update bioconductor-sbgnview.data

To create a new environment, run:

mamba create --name myenvname bioconductor-sbgnview.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-sbgnview.data:<tag>

(see `bioconductor-sbgnview.data/tags`_ for valid values for ``<tag>``)

Download stats

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-sbgnview.data/README.html)