recipe bioconductor-gagedata

Auxillary data for gage package

Homepage:

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

License:

GPL (>=2.0)

Recipe:

/bioconductor-gagedata/meta.yaml

This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included.

package bioconductor-gagedata

(downloads) docker_bioconductor-gagedata

versions:
2.40.0-0,  2.38.0-0,  2.35.0-0,  2.32.0-1,  2.32.0-0,  2.30.0-0,  2.28.0-1,  2.28.0-0,  2.27.0-0, 

2.40.0-0,  2.38.0-0,  2.35.0-0,  2.32.0-1,  2.32.0-0,  2.30.0-0,  2.28.0-1,  2.28.0-0,  2.27.0-0,  2.26.0-0,  2.24.0-0,  2.22.0-1,  2.22.0-0,  2.20.0-0,  2.18.0-0,  2.16.0-1,  2.16.0-0,  2.14.0-0,  2.10.0-0,  2.8.0-0

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-gagedata

and update with::

   mamba update bioconductor-gagedata

To create a new environment, run:

mamba create --name myenvname bioconductor-gagedata

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-gagedata:<tag>

(see `bioconductor-gagedata/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-gagedata/README.html)