recipe bioconductor-summix

Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/Summix.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-summix/meta.yaml

This package contains the Summix2 method for estimating and adjusting for substructure in genetic summary allele frequency data. The function summix() estimates reference group proportions using a mixture model. The adjAF() function produces adjusted allele frequencies for an observed group with reference group proportions matching a target individual or sample. The summix_local() function estimates local ancestry mixture proportions and performs selection scans in genetic summary data.

package bioconductor-summix

(downloads) docker_bioconductor-summix

Versions:

2.8.0-0,  2.6.0-0,  2.4.0-0,  2.0.0-0,  1.0.0-0

Depends:

  • on r-base >=4.3,<4.4.0a0

  • on r-nloptr

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-summix

to add into an existing workspace instead, run:

pixi add bioconductor-summix

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-summix

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-summix

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-summix:<tag>

(see bioconductor-summix/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.

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Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-summix/README.html)