Package Recipe 'bioconductor-decoupler'

recipe bioconductor-decoupler

decoupleR: Ensemble of computational methods to infer biological activities from omics data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/decoupleR.html
License:: GPL-3 + file LICENSE
Recipe:: /bioconductor-decoupler/meta.yaml

Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. Here, we present decoupleR, a Bioconductor package containing different statistical methods to extract these signatures within a unified framework. decoupleR allows the user to flexibly test any method with any resource. It incorporates methods that take into account the sign and weight of network interactions. decoupleR can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.

package bioconductor-decoupler¶

Versions:

2.16.0-0, 2.12.0-0, 2.8.0-0, 2.6.0-0, 2.4.0-0, 2.0.0-0, 1.0.0-0

Depends:

on bioconductor-biocparallel >=1.44.0,<1.45.0
on r-base >=4.5,<4.6.0a0
on r-broom
on r-dplyr
on r-magrittr
on r-matrix
on r-parallelly
on r-purrr
on r-rlang
on r-stringr
on r-tibble
on r-tidyr
on r-tidyselect
on r-withr

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-decoupler

to add into an existing workspace instead, run:

pixi add bioconductor-decoupler

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-decoupler

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-decoupler

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-decoupler:<tag>

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