recipe bioconductor-gagedata

Auxillary data for gage package

Homepage:

https://bioconductor.org/packages/3.20/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:
2.48.0-0,  2.44.0-0,  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, 

2.48.0-0,  2.44.0-0,  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:

  • on bioconductor-data-packages >=20260207

  • on curl

  • on r-base >=4.5,<4.6.0a0

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-gagedata

to add into an existing workspace instead, run:

pixi add bioconductor-gagedata

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-gagedata

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-gagedata

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-gagedata:<tag>

(see bioconductor-gagedata/tags for valid values for <tag>).

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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