recipe bioconductor-oncoscanr

Secondary analyses of CNV data (HRD and more)

Homepage:

https://bioconductor.org/packages/3.18/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:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-magrittr:

depends r-readr:

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-oncoscanr

and update with::

   mamba update bioconductor-oncoscanr

To create a new environment, run:

mamba create --name myenvname bioconductor-oncoscanr

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-oncoscanr:<tag>

(see `bioconductor-oncoscanr/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/bioconductor-oncoscanr/README.html)