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 (3.21)
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] (ORCID:
Maintainer: Michael Olbrich <M.Olbrich at protonmail.com>
citation("MBECS")):
Installation
To install this package, start R (version "4.5") 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
| Reference Manual |
Details
| biocViews | BatchEffect, Microbiome, Normalization, QualityControl, ReportWriting, Software, Visualization |
| Version | 1.11.0 |
| 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 |
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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |