- recipe bioconductor-rvs
Computes estimates of the probability of related individuals sharing a rare variant
- Homepage:
- License:
GPL-2
- Recipe:
Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).
- package bioconductor-rvs¶
- Versions:
1.32.0-0,1.28.0-0,1.24.0-0,1.22.0-0,1.20.0-0,1.16.0-0,1.14.0-0,1.12.0-1,1.12.0-0,1.32.0-0,1.28.0-0,1.24.0-0,1.22.0-0,1.20.0-0,1.16.0-0,1.14.0-0,1.12.0-1,1.12.0-0,1.10.0-0,1.8.0-0,1.6.0-1,1.4.0-0- Depends:
on bioconductor-snpstats
>=1.60.0,<1.61.0on r-base
>=4.5,<4.6.0a0on r-genlib
on r-grain
on r-kinship2
on r-r.utils
- 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-rvs
to add into an existing workspace instead, run:
pixi add bioconductor-rvs
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-rvs
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-rvs
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-rvs:<tag>
(see bioconductor-rvs/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-rvs/README.html)
