recipe bioconductor-regionalpcs

Summarizing Regional Methylation with Regional Principal Components Analysis

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-regionalpcs/meta.yaml

Functions to summarize DNA methylation data using regional principal components. Regional principal components are computed using principal components analysis within genomic regions to summarize the variability in methylation levels across CpGs. The number of principal components is chosen using either the Marcenko-Pasteur or Gavish-Donoho method to identify relevant signal in the data.

package bioconductor-regionalpcs

(downloads) docker_bioconductor-regionalpcs

versions:

1.0.0-0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-pcatools:

>=2.14.0,<2.15.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-tibble:

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-regionalpcs

and update with::

   mamba update bioconductor-regionalpcs

To create a new environment, run:

mamba create --name myenvname bioconductor-regionalpcs

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-regionalpcs:<tag>

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

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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-regionalpcs/README.html)