recipe bioconductor-oncoscanr

Secondary analyses of CNV data (HRD and more)

Homepage:

https://bioconductor.org/packages/3.16/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

Versions:

1.0.0-0

Depends:

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• r-base >=4.2,<4.3.0a0

• r-magrittr

• r-readr

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-oncoscanr

and update with:

conda update bioconductor-oncoscanr

or 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

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