Package Recipe 'bioconductor-csdr'

recipe bioconductor-csdr

Differential gene co-expression

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

This package contains functionality to run differential gene co-expression across two different conditions. The algorithm is inspired by Voigt et al. 2017 and finds Conserved, Specific and Differentiated genes (hence the name CSD). This package include efficient and variance calculation by bootstrapping and Welford's algorithm.

package bioconductor-csdr¶

Versions:

1.16.0-0, 1.12.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-1, 1.4.0-0, 1.0.0-2, 1.0.0-1, 1.0.0-0

Depends:

on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-glue
on r-matrixstats
on r-rcpp
on r-rhpcblasctl
on r-wgcna >=1.74,<2.0a0

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-csdr

to add into an existing workspace instead, run:

pixi add bioconductor-csdr

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-csdr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-csdr

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-csdr:<tag>

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