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 r-base:

>=4.3,<4.4.0a0

depends r-nloptr:

requirements:

additional platforms:

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 bioconductor-summix

and update with::

   mamba update bioconductor-summix

To create a new environment, run:

mamba create --name myenvname bioconductor-summix

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/bioconductor-summix:<tag>

(see `bioconductor-summix/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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)