mbQTL

DOI: 10.18129/B9.bioc.mbQTL  

mbQTL: A package for SNP-Taxa mGWAS analysis

Bioconductor version: Release (3.17)

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] , Steven Schiff [aut], Joseph N Paulson [aut]

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

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("mbQTL")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("mbQTL")

 

HTML	R Script	MbQTL_Vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Metagenomics, Microbiome, Regression, SNP, Software, StatisticalMethod, WholeGenome
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.3.0)
Imports	MatrixEQTL, dplyr, ggplot2, readxl, stringr, tidyr, metagenomeSeq, pheatmap, broom, graphics, stats, methods
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	"https://github.com/Mercedeh66/mbQTL"
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	mbQTL_1.0.0.tar.gz
Windows Binary	mbQTL_1.0.0.zip
macOS Binary (x86_64)	mbQTL_1.0.0.tgz
macOS Binary (arm64)	mbQTL_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mbQTL
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mbQTL
Bioc Package Browser	https://code.bioconductor.org/browse/mbQTL/
Package Short Url	https://bioconductor.org/packages/mbQTL/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive