Package Recipe 'bioconductor-variancepartition'

recipe bioconductor-variancepartition

Quantify and interpret drivers of variation in multilevel gene expression experiments

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/variancePartition.html
License:: GPL-2
Recipe:: /bioconductor-variancepartition/meta.yaml
Links:: biotools: variancepartition

Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. Includes dream differential expression analysis for repeated measures.

package bioconductor-variancepartition¶

Versions:

1.40.1-0, 1.36.2-0, 1.32.2-0, 1.30.2-0, 1.28.0-0, 1.24.0-0, 1.22.0-0, 1.20.0-1, 1.20.0-0,

1.40.1-0, 1.36.2-0, 1.32.2-0, 1.30.2-0, 1.28.0-0, 1.24.0-0, 1.22.0-0, 1.20.0-1, 1.20.0-0, 1.18.0-0, 1.16.0-0, 1.14.1-0, 1.14.0-1, 1.12.3-0, 1.12.0-0, 1.10.4-0, 1.8.1-0

Depends:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-limma >=3.66.0,<3.67.0
on r-aod
on r-base >=4.5,<4.6.0a0
on r-corpcor
on r-fancova
on r-ggplot2
on r-gplots
on r-gtools
on r-iterators
on r-lme4 >=1.1.33
on r-lmertest
on r-mass
on r-matrix >=1.4.0
on r-matrixstats
on r-pbkrtest >=0.4-4
on r-rdpack
on r-reformulas
on r-remacor >=0.0.15
on r-reshape2
on r-rhpcblasctl
on r-rlang
on r-scales

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-variancepartition

to add into an existing workspace instead, run:

pixi add bioconductor-variancepartition

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-variancepartition

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-variancepartition

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-variancepartition:<tag>

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