batchCorr
This is thereleased version of batchCorr; for the devel version, seebatchCorr.
Within And Between Batch Correction Of LC-MS Metabolomics Data
Bioconductor version: Release (3.22)
From the perspective of metabolites as the continuation of the central dogma of biology, metabolomics provides the closest link to many phenotypes of interest. This makes metabolomics research promising in teasing apart the complexities of living systems. However, due to experimental reasons, the data includes non-biological variation which limits quality and reproducibility, especially if the data is obtained from several batches. The batchCorr package reduces unwanted variation by way of between-batch alignment, within-batch drift correction and between-batch normalization using batch-specific quality control samples and long-term reference QC samples. Please see the associated article for more thorough descriptions of algorithms.
Author: Anton Ribbenstedt [cre]
ORCID: 0000-0002-9985-5644, Carl Brunius [aut] ORCID: 0000-0003-3957-870X, Vilhelm Suksi [aut]
Maintainer: Anton Ribbenstedt <parasitetwin at gmail.com>
citation("batchCorr")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("batchCorr")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("batchCorr")| Introduction.html | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect,BiomedicalInformatics,MassSpectrometry,Metabolomics,Normalization,QualityControl,Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| License | GPL-2 |
| Depends | R (>= 4.4.0),SummarizedExperiment |
| Imports | reshape,mclust,BiocParallel, methods |
| System Requirements | |
| URL | https://github.com/MetaboComp/batchCorr |
| Bug Reports | https://github.com/MetaboComp/batchCorr/issues |
See More
| Suggests | BiocStyle,knitr,testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | notameViz |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | batchCorr_1.0.0.tar.gz |
| Windows Binary (x86_64) | batchCorr_1.0.0.zip |
| macOS Binary (x86_64) | batchCorr_1.0.0.tgz |
| macOS Binary (arm64) | batchCorr_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/batchCorr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/batchCorr |
| Bioc Package Browser | https://code.bioconductor.org/browse/batchCorr/ |
| Package Short Url | https://bioconductor.org/packages/batchCorr/ |
| Package Downloads Report | Download Stats |