Package Recipe 'bioconductor-pareg'

recipe bioconductor-pareg

Pathway enrichment using a regularized regression approach

Homepage:: https://bioconductor.org/packages/3.18/bioc/html/pareg.html
License:: GPL-3
Recipe:: /bioconductor-pareg/meta.yaml

Compute pathway enrichment scores while accounting for term-term relations. This package uses a regularized multiple linear regression to regress differential expression p-values obtained from multi-condition experiments on a pathway membership matrix. By doing so, it is able to incorporate additional biological knowledge into the enrichment analysis and to estimate pathway enrichment scores more robustly.

package bioconductor-pareg¶

Versions:

1.6.0-0, 1.2.0-0

Depends:

on bioconductor-basilisk >=1.14.0,<1.15.0
on bioconductor-dose >=3.28.0,<3.29.0
on r-base >=4.3,<4.4.0a0
on r-devtools
on r-dofuture
on r-dorng
on r-dplyr
on r-foreach
on r-future
on r-ggplot2
on r-ggraph
on r-ggrepel
on r-glue
on r-hms
on r-igraph
on r-keras
on r-logger
on r-magrittr
on r-matrix
on r-nloptr
on r-progress
on r-proxy
on r-purrr
on r-reticulate
on r-rlang
on r-stringr
on r-tensorflow >=2.2.0
on r-tfprobability >=0.10.0
on r-tibble
on r-tidygraph
on r-tidyr

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-pareg

to add into an existing workspace instead, run:

pixi add bioconductor-pareg

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-pareg

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-pareg

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-pareg:<tag>

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