Package Recipe 'bioconductor-multiwgcna'

recipe bioconductor-multiwgcna

multiWGCNA

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/multiWGCNA.html
License:: GPL-3
Recipe:: /bioconductor-multiwgcna/meta.yaml

An R package for deeping mining gene co-expression networks in multi-trait expression data. Provides functions for analyzing, comparing, and visualizing WGCNA networks across conditions. multiWGCNA was designed to handle the common case where there are multiple biologically meaningful sample traits, such as disease vs wildtype across development or anatomical region.

package bioconductor-multiwgcna¶

Versions:

1.7.0-0, 1.4.0-0, 1.0.0-0

Depends:

on bioconductor-dcanr >=1.26.0,<1.27.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-cowplot
on r-data.table
on r-dplyr
on r-flashclust
on r-ggalluvial
on r-ggplot2
on r-ggrepel
on r-igraph
on r-patchwork
on r-readr
on r-reshape2
on r-scales
on r-stringr
on r-wgcna

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-multiwgcna

to add into an existing workspace instead, run:

pixi add bioconductor-multiwgcna

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-multiwgcna

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-multiwgcna

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-multiwgcna:<tag>

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