recipe bioconductor-lumi

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/lumi.html

License:

LGPL (>= 2)

Recipe:

/bioconductor-lumi/meta.yaml

Links:

biotools: lumi

The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.

package bioconductor-lumi

versions:

2.52.0-0,  2.50.0-0,  2.46.0-1,  2.44.0-0,  2.42.0-1,  2.42.0-0,  2.40.0-0,  2.38.0-0,  2.36.0-1, 

2.52.0-0,  2.50.0-0,  2.46.0-1,  2.44.0-0,  2.42.0-1,  2.42.0-0,  2.40.0-0,  2.38.0-0,  2.36.0-1,  2.34.0-0,  2.32.0-0,  2.30.0-0

depends bioconductor-affy:

>=1.78.0,<1.79.0

depends bioconductor-annotate:

>=1.78.0,<1.79.0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-methylumi:

>=2.46.0,<2.47.0

depends bioconductor-preprocesscore:

>=1.62.0,<1.63.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dbi:

depends r-kernsmooth:

depends r-lattice:

depends r-mass:

depends r-mgcv:

>=1.4-0

depends r-nleqslv:

depends r-rsqlite:

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-lumi

and update with::

   mamba update bioconductor-lumi

To create a new environment, run:

mamba create --name myenvname bioconductor-lumi

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-lumi:<tag>

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

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