proBatch
This is the development version of proBatch; for the stable release version, see proBatch.
All Bioconductor versions of proBatch
3.24 (devel), 3.23 (release), 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9
Tools for Diagnostics and Corrections of Batch Effects in Proteomics
Bioconductor version: 3.24 · Package version: 2.1.3
These tools facilitate batch effects analysis and correction in high-throughput experiments. It was developed primarily for mass-spectrometry proteomics (DIA/SWATH), but could also be applicable to most omic data with minor adaptations. The package contains functions for diagnostics (proteome/genome-wide and feature-level), correction (normalization and batch effects correction) and quality control. Non-linear fitting based approaches were also included to deal with complex, mass spectrometry-specific signal drifts.
Author: Jelena Cuklina [aut], Chloe H. Lee [aut], Patrick Pedrioli [aut], Olga Zolotareva [aut], Yuliya Burankova [cre]
Maintainer: Yuliya Burankova <yuliya.burankova at uni-hamburg.de>
Citation
From within R, enter citation("proBatch"):
Jelena Cuklina, Chloe H. Lee, Patrick Pedrioli, Olga Zolotareva. proBatch: Tools for Diagnostics and Corrections of Batch Effects in Proteomics. doi:10.18129/B9.bioc.proBatch, R package version 2.1.3, https://bioconductor.org/packages/proBatch.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("proBatch")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 2.1.3 |
| License | GPL-3 |
| URL | https://github.com/Freddsle/proBatch |
| Bug Reports | https://github.com/Freddsle/proBatch/issues |
| Last updated | 2026-08-01 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7 years) |
| Downloads rank | 1266 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | BatchEffect, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/proBatch/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("proBatch")| proBatch | HTML | R Script |
| ProBatchFeatures | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | proBatch_2.1.3.tar.gz |
| Windows binary (x86_64) | proBatch_2.1.3.zip |
| macOS binary (arm64) | proBatch_2.1.3.tgz |
| macOS binary (x86_64) | proBatch_2.1.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/proBatch |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/proBatch |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0)
Imports: Biobase, QFeatures, SummarizedExperiment, S4Vectors, corrplot, dplyr, data.table, ggfortify, ggplot2, graphics, grid, gridExtra, grDevices, lazyeval, lubridate, limma, magrittr, matrixStats, methods, pheatmap, preprocessCore, purrr, pvca, RColorBrewer, rlang, scales, splines, stats, sva, tidyr, tibble, tools, utils, viridis, wesanderson, withr, WGCNA
Suggests: BiocStyle, cowplot, ggplotify, knitr, rmarkdown, devtools, gtable, plotly, Rtsne, roxygen2, testthat (>= 3.2.0), spelling, HDF5Array, MASS, umap