recipe bioconductor-copynumber

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

Homepage

https://bioconductor.org/packages/3.12/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

Versions

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 >=0.36.0,<0.37.0

• bioconductor-genomicranges >=1.42.0,<1.43.0

• bioconductor-iranges >=2.24.0,<2.25.0

• bioconductor-s4vectors >=0.28.0,<0.29.0

• r-base >=4.0,<4.1.0a0

Required By

• hmftools-cobalt

• r-sequenza

• hmftools-amber

• r-eacon

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-copynumber

and update with:

conda update bioconductor-copynumber

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-copynumber:<tag>

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

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-copynumber/README.html)