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MBECS

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

Evaluation and correction of batch effects in microbiome data-sets


Bioconductor version: Development (3.19)

The Microbiome Batch Effect Correction Suite (MBECS) provides a set of functions to evaluate and mitigate unwated noise due to processing in batches. To that end it incorporates a host of batch correcting algorithms (BECA) from various packages. In addition it offers a correction and reporting pipeline that provides a preliminary look at the characteristics of a data-set before and after correcting for batch effects.

Author: Michael Olbrich [aut, cre]

Maintainer: Michael Olbrich <M.Olbrich at protonmail.com>

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

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("MBECS")

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("MBECS")
MBECS introduction HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, Microbiome, Normalization, QualityControl, ReportWriting, Software, Visualization
Version 1.7.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License Artistic-2.0
Depends R (>= 4.1)
Imports methods, magrittr, phyloseq, limma, lme4, lmerTest, pheatmap, rmarkdown, cluster, dplyr, ggplot2, gridExtra, ruv, sva, tibble, tidyr, vegan, stats, utils, Matrix
System Requirements
URL https://github.com/rmolbrich/MBECS
Bug Reports https://github.com/rmolbrich/MBECS/issues/new
See More
Suggests knitr, markdown, BiocStyle, testthat (>= 3.0.0)
Linking To
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Build Report Build Report

Package Archives

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

Source Package MBECS_1.7.0.tar.gz
Windows Binary MBECS_1.7.0.zip (64-bit only)
macOS Binary (x86_64) MBECS_1.7.0.tgz
macOS Binary (arm64) MBECS_1.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MBECS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MBECS
Bioc Package Browser https://code.bioconductor.org/browse/MBECS/
Package Short Url https://bioconductor.org/packages/MBECS/
Package Downloads Report Download Stats