recipe r-cghseg

Dedicated to the analysis of CGH (Comparative Genomic Hybridization) array profiles using segmentation models. 'cghseg' package is intended to detect breakpoints from CGH profiles. It can handle both single and multiple profiles analysis, to perform segmentation, normalization and calling. Methods for joint segmentation are described in Picard and al. (2011).

Homepage:

https://CRAN.R-project.org/package=cghseg

License:

GPL3 / GPL (>= 2)

Recipe:

/r-cghseg/meta.yaml

package r-cghseg

(downloads) docker_r-cghseg

versions:

1.0.5-3,  1.0.5-2,  1.0.5-1,  1.0.5-0

depends r-base:

>=4.0,<4.1.0a0

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 r-cghseg

and update with::

   mamba update r-cghseg

To create a new environment, run:

mamba create --name myenvname r-cghseg

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/r-cghseg:<tag>

(see `r-cghseg/tags`_ for valid values for ``<tag>``)

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Link to this page

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