recipe bioconductor-copynumber

Segmentation of single- and multi-track copy number data by penalized least squares regression.

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/copynumber.html

License:

Artistic-2.0

Recipe:

/bioconductor-copynumber/meta.yaml

Links:

biotools: copynumber

Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.

package bioconductor-copynumber

(downloads) docker_bioconductor-copynumber

versions:
1.38.0-1,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1, 

1.38.0-1,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-0

depends bioconductor-biocgenerics:

depends bioconductor-genomicranges:

1.58.0.*

depends bioconductor-iranges:

depends bioconductor-s4vectors:

depends r-base:

>=4.4,<4.5.0a0

requirements:

additional platforms:

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-copynumber

and update with::

   mamba update bioconductor-copynumber

To create a new environment, run:

mamba create --name myenvname bioconductor-copynumber

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-copynumber:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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