recipe bioconductor-purecn

Copy number calling and SNV classification using targeted short read sequencing

Homepage

https://bioconductor.org/packages/3.11/bioc/html/PureCN.html

License

Artistic-2.0

Recipe

/bioconductor-purecn/meta.yaml

Links

biotools: purecn

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

package bioconductor-purecn

Versions

1.18.0-0,  1.16.0-2,  1.16.0-1,  1.16.0-0,  1.14.2-0,  1.14.0-0,  1.13.1-2,  1.12.1-0,  1.11.20-2, 

1.18.0-0,  1.16.0-2,  1.16.0-1,  1.16.0-0,  1.14.2-0,  1.14.0-0,  1.13.1-2,  1.12.1-0,  1.11.20-2,  1.11.20-1,  1.11.13-1,  1.11.13-0,  1.8.0-0,  1.6.3-0

Depends

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-biostrings >=2.56.0,<2.57.0

• bioconductor-dnacopy >=1.62.0,<1.63.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicfeatures >=1.40.0,<1.41.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-rhdf5 >=2.32.0,<2.33.0

• bioconductor-rsamtools >=2.4.0,<2.5.0

• bioconductor-rtracklayer >=1.48.0,<1.49.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• bioconductor-variantannotation >=1.34.0,<1.35.0

• r-base >=4.0,<4.1.0a0

• r-data.table

• r-futile.logger

• r-ggplot2

• r-gridextra

• r-matrix

• r-rcolorbrewer

• r-vgam

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-purecn

and update with:

conda update bioconductor-purecn

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-purecn:<tag>

(see bioconductor-purecn/tags for valid values for <tag>)

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/bioconductor-purecn/README.html)