recipe bioconductor-oncoscanr

Secondary analyses of CNV data (HRD and more)

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/oncoscanR.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-oncoscanr/meta.yaml

The software uses the copy number segments from a text file and identifies all chromosome arms that are globally altered and computes various genome-wide scores. The following HRD scores (characteristic of BRCA-mutated cancers) are included: LST, HR-LOH, nLST and gLOH. the package is tailored for the ThermoFisher Oncoscan assay analyzed with their Chromosome Alteration Suite (ChAS) but can be adapted to any input.

package bioconductor-oncoscanr

(downloads) docker_bioconductor-oncoscanr

Versions:

1.12.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-0

Depends:

  • on bioconductor-genomicranges >=1.62.0,<1.63.0

  • on bioconductor-iranges >=2.44.0,<2.45.0

  • on bioconductor-s4vectors >=0.48.0,<0.49.0

  • on r-base >=4.5,<4.6.0a0

  • on r-magrittr

  • on r-readr

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-oncoscanr

to add into an existing workspace instead, run:

pixi add bioconductor-oncoscanr

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-oncoscanr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-oncoscanr

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-oncoscanr:<tag>

(see bioconductor-oncoscanr/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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Render an install-with-bioconda badge with the following MarkDown:

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