recipe bioconductor-decoupler

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

Homepage:

https://bioconductor.org/packages/3.18/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:

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

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends r-base:

>=4.4,<4.5.0a0

depends r-broom:

depends r-dplyr:

depends r-magrittr:

depends r-matrix:

depends r-parallelly:

depends r-purrr:

depends r-rlang:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

depends r-tidyselect:

depends r-withr:

requirements:

additional platforms:

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-decoupler

and update with::

   mamba update bioconductor-decoupler

To create a new environment, run:

mamba create --name myenvname bioconductor-decoupler

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-decoupler:<tag>

(see `bioconductor-decoupler/tags`_ for valid values for ``<tag>``)

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