recipe bioconductor-beadarray

Quality assessment and low-level analysis for Illumina BeadArray data

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-beadarray/meta.yaml

Links:

biotools: beadarray

The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

package bioconductor-beadarray

versions:

2.50.0-0,  2.48.0-1,  2.48.0-0,  2.44.0-2,  2.44.0-1,  2.44.0-0,  2.42.0-0,  2.40.0-1,  2.40.0-0, 

2.50.0-0,  2.48.0-1,  2.48.0-0,  2.44.0-2,  2.44.0-1,  2.44.0-0,  2.42.0-0,  2.40.0-1,  2.40.0-0,  2.38.0-0,  2.36.0-0,  2.34.0-1,  2.32.0-0,  2.30.0-0,  2.28.0-0,  2.26.1-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-beaddatapackr:

>=1.52.0,<1.53.0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-illuminaio:

>=0.42.0,<0.43.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-limma:

>=3.56.0,<3.57.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-hexbin:

depends r-reshape2:

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-beadarray

and update with::

   mamba update bioconductor-beadarray

To create a new environment, run:

mamba create --name myenvname bioconductor-beadarray

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-beadarray:<tag>

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

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