- recipe bioconductor-asafe
Ancestry Specific Allele Frequency Estimation
- Homepage:
- License:
Artistic-2.0
- Recipe:
- Links:
biotools: asafe, doi: 10.1093/bioinformatics/btw220
Given admixed individuals' bi-allelic SNP genotypes and ancestry pairs (where each ancestry can take one of three values) for multiple SNPs, perform an EM algorithm to deal with the fact that SNP genotypes are unphased with respect to ancestry pairs, in order to estimate ancestry-specific allele frequencies for all SNPs.
- package bioconductor-asafe¶
- Versions:
1.36.0-0,1.32.0-0,1.28.0-0,1.26.0-0,1.24.0-0,1.20.0-0,1.18.0-0,1.16.0-1,1.16.0-0,1.36.0-0,1.32.0-0,1.28.0-0,1.26.0-0,1.24.0-0,1.20.0-0,1.18.0-0,1.16.0-1,1.16.0-0,1.14.0-0,1.12.0-0,1.10.0-1,1.10.0-0,1.8.0-0,1.6.0-0,1.4.0-0,1.2.0-0- Depends:
on r-base
>=4.5,<4.6.0a0
- 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 bioconductor-asafe
to add into an existing workspace instead, run:
pixi add bioconductor-asafe
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 bioconductor-asafe
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-asafe
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/bioconductor-asafe:<tag>
(see bioconductor-asafe/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/bioconductor-asafe/README.html)
