recipe bioconductor-cn.farms

cn.FARMS - factor analysis for copy number estimation

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/cn.farms.html

License:

LGPL (>= 2.0)

Recipe:

/bioconductor-cn.farms/meta.yaml

Links:

biotools: cn.farms, doi: 10.1093/nar/gkr197

This package implements the cn.FARMS algorithm for copy number variation (CNV) analysis. cn.FARMS allows to analyze the most common Affymetrix (250K-SNP6.0) array types, supports high-performance computing using snow and ff.

package bioconductor-cn.farms

versions:

1.50.0-0,  1.48.0-0,  1.46.0-1,  1.46.0-0,  1.42.0-2,  1.42.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-1, 

1.50.0-0,  1.48.0-0,  1.46.0-1,  1.46.0-0,  1.42.0-2,  1.42.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-1,  1.38.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-0

depends bioconductor-affxparser:

>=1.74.0,<1.75.0

depends bioconductor-affxparser:

>=1.74.0,<1.75.0a0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0a0

depends bioconductor-dnacopy:

>=1.76.0,<1.77.0

depends bioconductor-dnacopy:

>=1.76.0,<1.77.0a0

depends bioconductor-oligo:

>=1.66.0,<1.67.0

depends bioconductor-oligo:

>=1.66.0,<1.67.0a0

depends bioconductor-oligoclasses:

>=1.64.0,<1.65.0

depends bioconductor-oligoclasses:

>=1.64.0,<1.65.0a0

depends bioconductor-preprocesscore:

>=1.64.0,<1.65.0

depends bioconductor-preprocesscore:

>=1.64.0,<1.65.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-dbi:

depends r-ff:

depends r-lattice:

depends r-snow:

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-cn.farms

and update with::

   mamba update bioconductor-cn.farms

To create a new environment, run:

mamba create --name myenvname bioconductor-cn.farms

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-cn.farms:<tag>

(see `bioconductor-cn.farms/tags`_ for valid values for ``<tag>``)

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