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/3.18/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:

3.40.0-0,  3.38.0-0,  3.36.0-1,  3.36.0-0,  3.32.0-2,  3.32.0-1,  3.32.0-0,  3.30.0-0,  3.28.0-1, 

3.40.0-0,  3.38.0-0,  3.36.0-1,  3.36.0-0,  3.32.0-2,  3.32.0-1,  3.32.0-0,  3.30.0-0,  3.28.0-1,  3.28.0-0,  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:

>=2.62.0,<2.63.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0a0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-biomart:

>=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 r-base:

>=4.3,<4.4.0a0

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 bioconductor-vegamc

and update with::

   mamba update bioconductor-vegamc

To create a new environment, run:

mamba create --name myenvname bioconductor-vegamc

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-vegamc:<tag>

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

Download stats

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