MBECS
This is the released version of MBECS; for the devel version, see MBECS.
Evaluation and correction of batch effects in microbiome data-sets
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.16.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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 | MBECS_1.16.0.tar.gz |
| Windows Binary (x86_64) | MBECS_1.16.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | MBECS_1.16.0.tgz |
| macOS Binary (sonoma-arm64) | MBECS_1.16.0.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 |