BDMMAcorrect

DOI: 10.18129/B9.bioc.BDMMAcorrect    

Meta-analysis for the metagenomic read counts data from different cohorts

Bioconductor version: Release (3.11)

Metagenomic sequencing techniques enable quantitative analyses of the microbiome. However, combining the microbial data from these experiments is challenging due to the variations between experiments. The existing methods for correcting batch effects do not consider the interactions between variables—microbial taxa in microbial studies—and the overdispersion of the microbiome data. Therefore, they are not applicable to microbiome data. We develop a new method, Bayesian Dirichlet-multinomial regression meta-analysis (BDMMA), to simultaneously model the batch effects and detect the microbial taxa associated with phenotypes. BDMMA automatically models the dependence among microbial taxa and is robust to the high dimensionality of the microbiome and their association sparsity.

Author: ZHENWEI DAI <daizwhao at gmail.com>

Maintainer: ZHENWEI DAI <daizwhao at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("BDMMAcorrect")

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("BDMMAcorrect")

 

PDF	R Script	BDMMAcorrect_user_guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, Bayesian, ImmunoOncology, Microbiome, Software
Version	1.6.0
In Bioconductor since	BioC 3.8 (R-3.5) (2 years)
License	GPL (>= 2)
Depends	R (>= 3.5), vegan, ellipse, ggplot2, ape, SummarizedExperiment
Imports	Rcpp (>= 0.12.12), RcppArmadillo, RcppEigen, stats
LinkingTo	Rcpp, RcppArmadillo, RcppEigen
Suggests	knitr, rmarkdown, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
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Build Report

Package Archives

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

Source Package	BDMMAcorrect_1.6.0.tar.gz
Windows Binary	BDMMAcorrect_1.6.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	BDMMAcorrect_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BDMMAcorrect
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BDMMAcorrect
Package Short Url	https://bioconductor.org/packages/BDMMAcorrect/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive