Package Recipe 'bioconductor-gwas.bayes'

recipe bioconductor-gwas.bayes

Bayesian analysis of Gaussian GWAS data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/GWAS.BAYES.html
License:: GPL-3 + file LICENSE
Recipe:: /bioconductor-gwas.bayes/meta.yaml

This package is built to perform GWAS analysis using Bayesian techniques. Currently, GWAS.BAYES has functionality for the implementation of BICOSS (Williams, J., Ferreira, M. A., and Ji, T. (2022). BICOSS: Bayesian iterative conditional stochastic search for GWAS. BMC Bioinformatics), BGWAS (Williams, J., Xu, S., Ferreira, M. A.. (2023) "BGWAS: Bayesian variable selection in linear mixed models with nonlocal priors for genome-wide association studies." BMC Bioinformatics), and GINA. All methods currently are for the analysis of Gaussian phenotypes The research related to this package was supported in part by National Science Foundation awards DMS 1853549, DMS 1853556, and DMS 2054173.

package bioconductor-gwas.bayes¶

Versions:

1.20.0-0, 1.16.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-1, 1.8.0-0, 1.4.0-2, 1.4.0-1, 1.4.0-0,

1.20.0-0, 1.16.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-1, 1.8.0-0, 1.4.0-2, 1.4.0-1, 1.4.0-0, 1.1.0-0, 1.0.0-2, 1.0.0-1

Depends:

on bioconductor-limma >=3.66.0,<3.67.0
on r-base >=4.5,<4.6.0a0
on r-caret >=6.0-86
on r-ga >=3.2
on r-mass >=7.3-58.1
on r-matrix >=1.2-18
on r-memoise >=1.1.0

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-gwas.bayes

to add into an existing workspace instead, run:

pixi add bioconductor-gwas.bayes

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-gwas.bayes

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-gwas.bayes

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-gwas.bayes:<tag>

(see bioconductor-gwas.bayes/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:

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