DOI: 10.18129/B9.bioc.proBatch  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Bioconductor version: Release (3.17)

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 <chuklina.jelena at>, Chloe H. Lee <chloe.h.lee94 at>, Patrick Pedrioli <pedrioli at>

Maintainer: Chloe H. Lee <chloe.h.lee94 at>

Citation (from within R, enter citation("proBatch")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


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biocViews BatchEffect, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, Software
Version 1.15.1
In Bioconductor since BioC 3.9 (R-3.6) (4.5 years)
License GPL-3
Depends R (>= 3.6)
Imports Biobase, corrplot, dplyr, data.table, ggfortify, ggplot2, grDevices, lazyeval, lubridate, magrittr, pheatmap, preprocessCore, purrr, pvca, RColorBrewer, reshape2, rlang, scales, stats, sva, tidyr, tibble, tools, utils, viridis, wesanderson, WGCNA
Suggests knitr, rmarkdown, devtools, ggpubr, gtable, gridExtra, roxygen2, testthat (>= 2.1.0), spelling
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