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 (3.20)

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>

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

Installation

To install this package, start R (version "4.4") 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
NEWS Text
LICENSE Text

Details

biocViews Metagenomics, Microbiome, Regression, SNP, Software, StatisticalMethod, WholeGenome
Version 1.5.0
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"
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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) mbQTL_1.5.0.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/
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