recipe ascat

ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy (Figure 1). ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell, expressed as multiples of haploid genomes) from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome).

Homepage:

https://www.crick.ac.uk/research/a-z-researchers/researchers-v-y/peter-van-loo/software/

Developer docs:

https://github.com/Crick-CancerGenomics/ascat

License:

GPL / GPL-3.0

Recipe:

/ascat/meta.yaml

Links:

biotools: ascat, doi: 10.1073/pnas.1009843107

package ascat

Versions:

3.1.1-0,  3.0.0-1,  3.0.0-0,  2.5.2-4,  2.5.2-3,  2.5.2-2,  2.5.2-1,  2.5.2-0,  2.5.1-2, 

3.1.1-0,  3.0.0-1,  3.0.0-0,  2.5.2-4,  2.5.2-3,  2.5.2-2,  2.5.2-1,  2.5.2-0,  2.5.1-2,  2.5.1-0,  2.5-0

Depends:

• bioconductor-genomicranges

• bioconductor-iranges

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-doparallel

• r-foreach

• r-r.devices

• r-r.utils

• r-rcolorbrewer

Required By:

• r-eacon

Installation

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

conda install ascat

and update with:

conda update ascat

or use the docker container:

docker pull quay.io/biocontainers/ascat:<tag>

(see ascat/tags for valid values for <tag>)

Download stats

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