- 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).
- package ascat¶
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends r-base:
- depends r-data.table:
- depends r-doparallel:
- depends r-foreach:
- depends r-r.devices:
- depends r-r.utils:
- depends r-rcolorbrewer:
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 ascat and update with:: mamba update ascat
To create a new environment, run:
mamba create --name myenvname ascat
myenvnamebeing 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/ascat:<tag> (see `ascat/tags`_ for valid values for ``<tag>``)