recipe bioconductor-pvca

Principal Variance Component Analysis (PVCA)

Homepage:

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

License:

LGPL (>= 2.0)

Recipe:

/bioconductor-pvca/meta.yaml

Links:

biotools: pvca, doi: 10.1002/9780470685983.ch12

This package contains the function to assess the batch sourcs by fitting all "sources" as random effects including two-way interaction terms in the Mixed Model(depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book "Batch Effects and Noise in Microarray Experiements, chapter 12.

package bioconductor-pvca

(downloads) docker_bioconductor-pvca

versions:
1.42.0-0,  1.40.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-0, 

1.42.0-0,  1.40.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-vsn:

>=3.70.0,<3.71.0

depends r-base:

>=4.3,<4.4.0a0

depends r-lme4:

depends r-matrix:

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-pvca

and update with::

   mamba update bioconductor-pvca

To create a new environment, run:

mamba create --name myenvname bioconductor-pvca

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-pvca:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda 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-pvca/README.html)