-
recipe
bioconductor-purecn¶ Copy number calling and SNV classification using targeted short read sequencing
- Homepage
https://bioconductor.org/packages/3.10/bioc/html/PureCN.html
- License
Artistic-2.0
- Recipe
- 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
1.16.0-1, 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 >=0.32.0,<0.33.0
bioconductor-biostrings >=2.54.0,<2.55.0
bioconductor-dnacopy >=1.60.0,<1.61.0
bioconductor-genomeinfodb >=1.22.0,<1.23.0
bioconductor-genomicfeatures >=1.38.0,<1.39.0
bioconductor-genomicranges >=1.38.0,<1.39.0
bioconductor-iranges >=2.20.0,<2.21.0
bioconductor-rhdf5 >=2.30.0,<2.31.0
bioconductor-rsamtools >=2.2.0,<2.3.0
bioconductor-rtracklayer >=1.46.0,<1.47.0
bioconductor-s4vectors >=0.24.0,<0.25.0
bioconductor-summarizedexperiment >=1.16.0,<1.17.0
bioconductor-variantannotation >=1.32.0,<1.33.0
r-base >=3.6,<3.7.0a0
- 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:
[](http://bioconda.github.io/recipes/bioconductor-purecn/README.html)