MBECS

DOI: 10.18129/B9.bioc.MBECS    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see MBECS.

Evaluation and correction of batch effects in microbiome data-sets

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	MBECS introduction
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, Microbiome, Normalization, QualityControl, ReportWriting, Software, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 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
LinkingTo
Suggests	knitr, markdown, BiocStyle, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/rmolbrich/MBECS
BugReports	https://github.com/rmolbrich/MBECS/issues/new
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MBECS_1.0.0.tar.gz
Windows Binary	MBECS_1.0.0.zip
macOS Binary (x86_64)	MBECS_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MBECS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MBECS
Package Short Url	https://bioconductor.org/packages/MBECS/
Package Downloads Report	Download Stats