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:

1.36.2-0,  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, 

1.36.2-0,  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 bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-limma:

>=3.62.1,<3.63.0

depends r-aod:

depends r-base:

>=4.4,<4.5.0a0

depends r-corpcor:

depends r-fancova:

depends r-ggplot2:

depends r-gplots:

depends r-iterators:

depends r-lme4:

>=1.1.33

depends r-lmertest:

depends r-mass:

depends r-matrix:

>=1.4.0

depends r-matrixstats:

depends r-pbkrtest:

>=0.4-4

depends r-rdpack:

depends r-remacor:

>=0.0.15

depends r-reshape2:

depends r-rhpcblasctl:

depends r-rlang:

depends r-scales:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-variancepartition

and update with::

   mamba update bioconductor-variancepartition

To create a new environment, run:

mamba create --name myenvname bioconductor-variancepartition

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-variancepartition:<tag>

(see `bioconductor-variancepartition/tags`_ for valid values for ``<tag>``)

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