Package Recipe 'bioconductor-drugvsdisease'

recipe bioconductor-drugvsdisease

Comparison of disease and drug profiles using Gene set Enrichment Analysis

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/DrugVsDisease.html
License:: GPL-3
Recipe:: /bioconductor-drugvsdisease/meta.yaml
Links:: biotools: drugvsdisease, doi: 10.1038/nmeth.3252

This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Network visualisation of significant scores are output in Cytoscape format.

package bioconductor-drugvsdisease¶

Versions:

2.52.0-0, 2.48.0-0, 2.44.0-0, 2.42.0-0, 2.40.0-0, 2.36.0-0, 2.34.0-0, 2.32.0-1, 2.32.0-0,

2.52.0-0, 2.48.0-0, 2.44.0-0, 2.42.0-0, 2.40.0-0, 2.36.0-0, 2.34.0-0, 2.32.0-1, 2.32.0-0, 2.30.0-0, 2.28.0-1, 2.26.0-1, 2.24.2-0, 2.22.0-0, 2.20.1-0

Depends:

on bioconductor-affy >=1.88.0,<1.89.0
on bioconductor-annotate >=1.88.0,<1.89.0
on bioconductor-arrayexpress >=1.70.0,<1.71.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biomart >=2.66.0,<2.67.0
on bioconductor-cmap2data >=1.46.0,<1.47.0
on bioconductor-drugvsdiseasedata >=1.46.0,<1.47.0
on bioconductor-geoquery >=2.78.0,<2.79.0
on bioconductor-hgu133a.db >=3.13.0,<3.14.0
on bioconductor-hgu133a2.db >=3.13.0,<3.14.0
on bioconductor-hgu133plus2.db >=3.13.0,<3.14.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-qvalue >=2.42.0,<2.43.0
on r-base >=4.5,<4.6.0a0
on r-runit
on r-xtable

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-drugvsdisease

to add into an existing workspace instead, run:

pixi add bioconductor-drugvsdisease

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-drugvsdisease

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-drugvsdisease

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-drugvsdisease:<tag>

(see bioconductor-drugvsdisease/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-drugvsdisease/README.html)