recipe r-dinamic.duo

In tumor tissue, underlying genomic instability can lead to DNA copy number alterations, e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the genome, whereas recurrent alterations are observed in the same genomic region across multiple independent samples, perhaps because they provide a selective growth advantage. Here we use cyclic shift permutations to identify recurrent copy number alterations in a single cohort or recurrent copy number differences in two cohorts based on a common set of genomic markers. Additional functionality is provided to perform downstream analyses, including the creation of summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al. (2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al. (2015) <doi:10.1093/biomet/asv046>. A manuscript based on DiNAMIC.Duo is currently under development.

Homepage:

https://CRAN.R-project.org/package=DiNAMIC.Duo

License:

GPL3 / GPL-3.0-only

Recipe:

/r-dinamic.duo/meta.yaml

package r-dinamic.duo

(downloads) docker_r-dinamic.duo

versions:

1.0.2-2,  1.0.2-1,  1.0.2-0,  1.0.1-1,  1.0.1-0

depends bioconductor-biomart:

depends r-base:

>=4.3,<4.4.0a0

depends r-dinamic:

depends r-plyr:

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-dinamic.duo

and update with::

   mamba update r-dinamic.duo

To create a new environment, run:

mamba create --name myenvname r-dinamic.duo

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-dinamic.duo:<tag>

(see `r-dinamic.duo/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an install-with-bioconda 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/r-dinamic.duo/README.html)