MBECS

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see MBECS.

Evaluation and correction of batch effects in microbiome data-sets

Bioconductor version: 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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BatchEffect, Microbiome, Normalization, QualityControl, ReportWriting, Software, Visualization

Version 1.8.0

In Bioconductor since BioC 3.15 (R-4.2) (2.5 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

Suggests knitr, markdown, BiocStyle, testthat (>= 3.0.0)

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package MBECS_1.8.0.tar.gz

Windows Binary (x86_64) MBECS_1.8.0.zip

macOS Binary (x86_64) MBECS_1.8.0.tgz

macOS Binary (arm64) MBECS_1.8.0.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/

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