Package Recipe 'bioconductor-metagxpancreas'

recipe bioconductor-metagxpancreas

Transcriptomic Pancreatic Cancer Datasets

Homepage:: https://bioconductor.org/packages/3.20/data/experiment/html/MetaGxPancreas.html
License:: Artistic-2.0
Recipe:: /bioconductor-metagxpancreas/meta.yaml

A collection of pancreatic Cancer transcriptomic datasets that are part of the MetaGxData package compendium. This package contains multiple pancreas cancer datasets that have been downloaded from various resources and turned into SummarizedExperiment objects. The details of how the authors normalized the data can be found in the experiment data section of the objects. Additionally, the location the data was obtained from can be found in the url variables of the experiment data portion of each SE.

package bioconductor-metagxpancreas¶

Versions:

1.30.0-0, 1.26.0-0, 1.22.0-0, 1.20.0-0, 1.18.0-0, 1.14.0-1, 1.14.0-0, 1.12.0-0, 1.10.0-1,

1.30.0-0, 1.26.0-0, 1.22.0-0, 1.20.0-0, 1.18.0-0, 1.14.0-1, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.10.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-1, 1.2.0-0

Depends:

on bioconductor-annotationhub >=4.0.0,<4.1.0
on bioconductor-data-packages >=20260207
on bioconductor-experimenthub >=3.0.0,<3.1.0
on bioconductor-impute >=1.84.0,<1.85.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
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-metagxpancreas

to add into an existing workspace instead, run:

pixi add bioconductor-metagxpancreas

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-metagxpancreas

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-metagxpancreas

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-metagxpancreas:<tag>

(see bioconductor-metagxpancreas/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.

Download stats¶

Link to this page¶

Render an 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-metagxpancreas/README.html)