recipe bioconductor-decoupler

decoupleR: Inferring biological activities from omics data using a collection of methods

Homepage

https://bioconductor.org/packages/3.14/bioc/html/decoupleR.html

License

GPL-3

Recipe

/bioconductor-decoupler/meta.yaml

Computational methods allow the extraction of mechanistic signatures from omics data based on prior knowledge resources, reducing the dimensionality of the data 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. Using decoupleR, we evaluated the performance of contemporary methods on transcriptomic and phospho-proteomic perturbation experiments.

package bioconductor-decoupler

Versions

2.0.0-0,  1.0.0-0

Depends

• bioconductor-aucell >=1.16.0,<1.17.0

• bioconductor-fgsea >=1.20.0,<1.21.0

• bioconductor-gsva >=1.42.0,<1.43.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• bioconductor-viper >=1.28.0,<1.29.0

• r-base >=4.1,<4.2.0a0

• r-broom

• r-dplyr

• r-magrittr

• r-matrix

• r-purrr

• r-ranger

• r-rlang

• r-robustrankaggreg

• r-rpart

• r-speedglm

• r-stringr

• r-tibble

• r-tidyr

• r-tidyselect

• r-withr

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-decoupler

and update with:

conda update bioconductor-decoupler

or use the docker container:

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

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

Download stats

Link to this page

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