Package Recipe 'bioconductor-mbqtl'

recipe bioconductor-mbqtl

mbQTL: A package for SNP-Taxa mGWAS analysis

Homepage:: https://bioconductor.org/packages/3.18/bioc/html/mbQTL.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-mbqtl/meta.yaml

mbQTL is a statistical R package for simultaneous 16srRNA,16srDNA (microbial) and variant, SNP, SNV (host) relationship, correlation, regression studies. We apply linear, logistic and correlation based statistics to identify the relationships of taxa, genus, species and variant, SNP, SNV in the infected host. We produce various statistical significance measures such as P values, FDR, BC and probability estimation to show significance of these relationships. Further we provide various visualization function for ease and clarification of the results of these analysis. The package is compatible with dataframe, MRexperiment and text formats.

package bioconductor-mbqtl¶

Versions:

1.10.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-metagenomeseq >=1.52.0,<1.53.0
on r-base >=4.5,<4.6.0a0
on r-broom
on r-dplyr
on r-ggplot2
on r-matrixeqtl
on r-pheatmap
on r-readxl
on r-stringr
on r-tidyr

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-mbqtl

to add into an existing workspace instead, run:

pixi add bioconductor-mbqtl

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-mbqtl

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-mbqtl

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-mbqtl:<tag>

(see bioconductor-mbqtl/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-mbqtl/README.html)