recipe bioconductor-qsvar

Generate Quality Surrogate Variable Analysis for Degradation Correction

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/qsvaR.html

License:

Artistic-2.0

Recipe:

/bioconductor-qsvar/meta.yaml

The qsvaR package contains functions for removing the effect of degration in rna-seq data from postmortem brain tissue. The package is equipped to help users generate principal components associated with degradation. The components can be used in differential expression analysis to remove the effects of degradation.

package bioconductor-qsvar

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-sva:

>=3.50.0,<3.51.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

requirements:

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-qsvar

and update with::

   mamba update bioconductor-qsvar

To create a new environment, run:

mamba create --name myenvname bioconductor-qsvar

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-qsvar:<tag>

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

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