mbQTL
mbQTL: A package for SNP-Taxa mGWAS analysis
Bioconductor version: Release (3.19)
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("mbQTL")):
Installation
To install this package, start R (version "4.4") 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")| MbQTL_Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Metagenomics, Microbiome, Regression, SNP, Software, StatisticalMethod, WholeGenome |
| Version | 1.4.0 |
| 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" |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | mbQTL_1.4.0.tar.gz |
| Windows Binary (x86_64) | mbQTL_1.4.0.zip |
| macOS Binary (x86_64) | mbQTL_1.4.0.tgz |
| macOS Binary (arm64) | mbQTL_1.4.0.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 |