recipe bioconductor-cnvgears

A Framework of Functions to Combine, Analize and Interpret CNVs Calling Results

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/CNVgears.html

License:

GPL-3

Recipe:

/bioconductor-cnvgears/meta.yaml

This package contains a set of functions to perform several type of processing and analysis on CNVs calling pipelines/algorithms results in an integrated manner and regardless of the raw data type (SNPs array or NGS). It provides functions to combine multiple CNV calling results into a single object, filter them, compute CNVRs (CNV Regions) and inheritance patterns, detect genic load, and more. The package is best suited for studies in human family-based cohorts.

package bioconductor-cnvgears

(downloads) docker_bioconductor-cnvgears

Versions:

1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

Depends:

  • on r-base >=4.3,<4.4.0a0

  • on r-data.table

  • on r-ggplot2

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 bioconductor-cnvgears

to add into an existing workspace instead, run:

pixi add bioconductor-cnvgears

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 bioconductor-cnvgears

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cnvgears

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/bioconductor-cnvgears:<tag>

(see bioconductor-cnvgears/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.

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