recipe bioconductor-acgh

Classes and functions for Array Comparative Genomic Hybridization data

Homepage:

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

License:

GPL-2.0-only

Recipe:

/bioconductor-acgh/meta.yaml

Links:

biotools: acgh, doi: 10.1093/bioinformatics/bti677

Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.

package bioconductor-acgh

versions:

1.80.0-1,  1.80.0-0,  1.78.0-0,  1.76.0-1,  1.76.0-0,  1.72.0-2,  1.72.0-1,  1.72.0-0,  1.70.0-0, 

1.80.0-1,  1.80.0-0,  1.78.0-0,  1.76.0-1,  1.76.0-0,  1.72.0-2,  1.72.0-1,  1.72.0-0,  1.70.0-0,  1.68.0-1,  1.68.0-0,  1.66.0-0,  1.64.0-0,  1.62.0-1,  1.60.0-0,  1.58.0-0,  1.56.0-0,  1.54.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0a0

depends bioconductor-multtest:

>=2.58.0,<2.59.0

depends bioconductor-multtest:

>=2.58.0,<2.59.0a0

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-cluster:

depends r-survival:

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-acgh

and update with::

   mamba update bioconductor-acgh

To create a new environment, run:

mamba create --name myenvname bioconductor-acgh

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-acgh:<tag>

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

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