recipe bioconductor-crlmm

Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-crlmm/meta.yaml

Links:

biotools: crlmm

Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms.

package bioconductor-crlmm

versions:

1.58.0-0,  1.56.0-1,  1.56.0-0,  1.52.0-2,  1.52.0-1,  1.52.0-0,  1.50.0-0,  1.48.0-1,  1.48.0-0, 

1.58.0-0,  1.56.0-1,  1.56.0-0,  1.52.0-2,  1.52.0-1,  1.52.0-0,  1.50.0-0,  1.48.0-1,  1.48.0-0,  1.46.0-0,  1.44.0-0,  1.42.0-1,  1.40.0-0,  1.38.0-0,  1.36.0-0

depends bioconductor-affyio:

>=1.70.0,<1.71.0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-illuminaio:

>=0.42.0,<0.43.0

depends bioconductor-limma:

>=3.56.0,<3.57.0

depends bioconductor-oligoclasses:

>=1.62.0,<1.63.0

depends bioconductor-preprocesscore:

>=1.62.0,<1.63.0

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-beanplot:

depends r-ellipse:

depends r-ff:

depends r-foreach:

depends r-lattice:

depends r-matrixstats:

depends r-mvtnorm:

depends r-rcppeigen:

>=0.3.1.2.1

depends r-vgam:

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-crlmm

and update with::

   mamba update bioconductor-crlmm

To create a new environment, run:

mamba create --name myenvname bioconductor-crlmm

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-crlmm:<tag>

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

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-crlmm/README.html)