- 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:
- Developer docs:
- License:
GPL3 / GPL-3.0-or-later
- Recipe:
- Links:
biotools: ascat, doi: 10.1073/pnas.1009843107
- package ascat¶
- Versions:
3.2.0-1,3.2.0-0,3.1.1-1,3.1.1-0,3.0.0-1,3.0.0-0,2.5.2-4,2.5.2-3,2.5.2-2,3.2.0-1,3.2.0-0,3.1.1-1,3.1.1-0,3.0.0-1,3.0.0-0,2.5.2-4,2.5.2-3,2.5.2-2,2.5.2-1,2.5.2-0,2.5.1-2,2.5.1-0,2.5-0- Depends:
on bioconductor-genomicranges
on bioconductor-iranges
on r-base
>=4.4,<4.5.0a0on r-data.table
on r-doparallel
on r-foreach
on r-r.devices
on r-r.utils
on r-rcolorbrewer
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install ascat
to add into an existing workspace instead, run:
pixi add ascat
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install ascat
Alternatively, to install into a new environment, run:
conda create -n envname ascat
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/ascat:<tag>
(see ascat/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/ascat/README.html)
