recipe bioconductor-vegamc

VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer

Homepage

https://bioconductor.org/packages/3.11/bioc/html/VegaMC.html

License

GPL-2

Recipe

/bioconductor-vegamc/meta.yaml

Links

biotools: vegamc, doi: 10.1093/bioinformatics/bts453

This package enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. VegaMC performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, VegaMC produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported.

package bioconductor-vegamc

Versions

3.26.0-0,  3.24.0-0,  3.22.0-1,  3.20.0-0,  3.18.0-0,  3.16.0-0

Depends

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-biomart >=2.44.0,<2.45.0

• bioconductor-genoset >=1.44.0,<1.45.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.3.0

• liblapack >=3.8.0,<3.9.0a0

• r-base >=4.0,<4.1.0a0

Required By

Installation

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

conda install bioconductor-vegamc

and update with:

conda update bioconductor-vegamc

or use the docker container:

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

(see bioconductor-vegamc/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-vegamc/README.html)