Package Recipe 'bioconductor-marker'

recipe bioconductor-marker

An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers

Homepage:: https://bioconductor.org/packages/3.22/bioc/html/markeR.html
License:: Artistic-2.0
Recipe:: /bioconductor-marker/meta.yaml

markeR is an R package that provides a modular and extensible framework for the systematic evaluation of gene sets as phenotypic markers using transcriptomic data. The package is designed to support both quantitative analyses and visual exploration of gene set behaviour across experimental and clinical phenotypes. It implements multiple methods, including score-based and enrichment approaches, and also allows the exploration of expression behaviour of individual genes. In addition, users can assess the similarity of their own gene sets against established collections (e.g., those from MSigDB), facilitating biological interpretation.

package bioconductor-marker¶

Versions:

1.0.0-0

Depends:

on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-fgsea >=1.36.0,<1.37.0
on bioconductor-limma >=3.66.0,<3.67.0
on r-base >=4.5,<4.6.0a0
on r-circlize
on r-effectsize
on r-ggh4x
on r-ggplot2
on r-ggpubr
on r-ggrepel
on r-gridextra
on r-msigdbr
on r-proc
on r-rcolorbrewer
on r-reshape2
on r-rstatix
on r-scales
on r-tibble

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-marker

to add into an existing workspace instead, run:

pixi add bioconductor-marker

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-marker

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-marker

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-marker:<tag>

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