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BDMMAcorrect

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

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


Bioconductor version: Development (3.19)

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>

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

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("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")
BDMMAcorrect_user_guide PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, Bayesian, ImmunoOncology, Microbiome, Software
Version 1.21.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL (>= 2)
Depends R (>= 3.5), vegan, ellipse, ggplot2, ape, SummarizedExperiment
Imports Rcpp (>= 0.12.12), RcppArmadillo, RcppEigen, stats
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Suggests knitr, rmarkdown, BiocGenerics
Linking To Rcpp, RcppArmadillo, RcppEigen
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Package Archives

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

Source Package BDMMAcorrect_1.21.0.tar.gz
Windows Binary BDMMAcorrect_1.21.0.zip (64-bit only)
macOS Binary (x86_64) BDMMAcorrect_1.21.0.tgz
macOS Binary (arm64) BDMMAcorrect_1.21.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BDMMAcorrect
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BDMMAcorrect
Bioc Package Browser https://code.bioconductor.org/browse/BDMMAcorrect/
Package Short Url https://bioconductor.org/packages/BDMMAcorrect/
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