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>
citation("MBECS")):
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")| MBECS introduction | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, Microbiome, Normalization, QualityControl, ReportWriting, Software, Visualization |
| Version | 1.0.0 |
| 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 | |
| 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 | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/MBECS/ |
| Package Short Url | https://bioconductor.org/packages/MBECS/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.15 | Source Archive |