mbQTL

This is the development version of mbQTL; for the stable release version, see mbQTL.

mbQTL: A package for SNP-Taxa mGWAS analysis

Bioconductor version: Development (3.21)

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.

Author: Mercedeh Movassagh [aut, cre] (ORCID: ), Steven Schiff [aut], Joseph N Paulson [aut]

Maintainer: Mercedeh Movassagh <mercedeh.movassagh at yale.edu>

Citation (from within R, enter citation("mbQTL")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("mbQTL")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Metagenomics, Microbiome, Regression, SNP, Software, StatisticalMethod, WholeGenome
Version	1.7.0
In Bioconductor since	BioC 3.17 (R-4.3) (1.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.3.0)
Imports	MatrixEQTL, dplyr, ggplot2, readxl, stringr, tidyr, metagenomeSeq, pheatmap, broom, graphics, stats, methods
System Requirements
URL	"https://github.com/Mercedeh66/mbQTL"

Suggests	knitr, rmarkdown, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/mbQTL
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mbQTL
Package Short Url	https://bioconductor.org/packages/mbQTL/
Package Downloads Report	Download Stats