BDMMAcorrect
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see BDMMAcorrect.
Meta-analysis for the metagenomic read counts data from different cohorts
Bioconductor version: 3.9
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("BDMMAcorrect")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| BDMMAcorrect_user_guide | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, Bayesian, ImmunoOncology, Microbiome, Software |
| Version | 1.2.0 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocGenerics |
| Linking To | Rcpp, RcppArmadillo, RcppEigen |
| 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 | BDMMAcorrect_1.2.0.tar.gz |
| Windows Binary | BDMMAcorrect_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | BDMMAcorrect_1.2.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |