Package Recipe 'r-dinamic.duo'

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¶

Versions:

1.0.4-0, 1.0.3-0, 1.0.2-3, 1.0.2-2, 1.0.2-1, 1.0.2-0, 1.0.1-1, 1.0.1-0

Depends:

on bioconductor-biomart
on libxml2
on r-base >=4.4,<4.5.0a0
on r-curl
on r-dinamic
on r-plyr

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install r-dinamic.duo

to add into an existing workspace instead, run:

pixi add r-dinamic.duo

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install r-dinamic.duo

Alternatively, to install into a new environment, run:

conda create -n envname r-dinamic.duo

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/r-dinamic.duo:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

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/r-dinamic.duo/README.html)