recipe bioconductor-affycoretools

Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-affycoretools/meta.yaml

Links:

biotools: affycoretools, doi: 10.1038/nmeth.3252

Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.

package bioconductor-affycoretools

versions:

1.74.0-0,  1.72.0-0,  1.70.0-0,  1.66.0-0,  1.64.0-0,  1.62.0-1,  1.62.0-0,  1.60.1-0,  1.58.0-0, 

1.74.0-0,  1.72.0-0,  1.70.0-0,  1.66.0-0,  1.64.0-0,  1.62.0-1,  1.62.0-0,  1.60.1-0,  1.58.0-0,  1.56.0-1,  1.54.0-0,  1.52.2-0,  1.50.6-0

depends bioconductor-affy:

>=1.80.0,<1.81.0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-gcrma:

>=2.74.0,<2.75.0

depends bioconductor-glimma:

>=2.12.0,<2.13.0

depends bioconductor-gostats:

>=2.68.0,<2.69.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-oligoclasses:

>=1.64.0,<1.65.0

depends bioconductor-reportingtools:

>=2.42.0,<2.43.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dbi:

depends r-ggplot2:

depends r-gplots:

depends r-hwriter:

depends r-lattice:

depends r-rsqlite:

depends r-xtable:

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-affycoretools

and update with::

   mamba update bioconductor-affycoretools

To create a new environment, run:

mamba create --name myenvname bioconductor-affycoretools

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-affycoretools:<tag>

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

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