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

Documentation:

https://github.com/VanLoo-lab/ascat/blob/v3.2.0/README.md

Developer docs:

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

License:

GPL3 / GPL-3.0-or-later

Recipe:

/ascat/meta.yaml

Links:

biotools: ascat, doi: 10.1073/pnas.1009843107

package ascat

versions:

3.2.0-0,  3.1.1-1,  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, 

3.2.0-0,  3.1.1-1,  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:

depends bioconductor-iranges:

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-doparallel:

depends r-foreach:

depends r-r.devices:

depends r-r.utils:

depends r-rcolorbrewer:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

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

with myenvname being 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>``)

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