ProteinBatcher
This is the development version of ProteinBatcher; to use it, please install the devel version of Bioconductor.
An end-to-end proteomics workflow with condition-aware imputation, flexible statistical modelling and interactive visualization
Bioconductor version: 3.24 · Package version: 0.99.7
ProteinBatcher provides utilities to read, validate, and harmonize quantitative proteomics result tables generated by DIA-NN from data-independent acquisition mass spectrometry experiments. The package enables batch processing of multiple DIA-NN output files, consistent handling of protein identifiers and associated metadata, and transformation of tabular data into analysis-ready formats. It facilitates downstream differential abundance analysis using linear modeling frameworks based on limma, with explicit support for multivariable experimental designs including batch effects and other confounding covariates, as well as correlation-aware designs via duplicateCorrelation.
Author: Aitor Moruno-Cuenca [aut, cre] 
, Dr. Sergi Sayols-Puig [ctb] , Dr. Bruna Oriol-Tordera [ctb] , Dr. Hiba Salim [dtc] , Dr. Francesc Fernández-Albert [ths] , Prof. Dr. Alexandre Perera-Lluna [ths] , Dr. Guadalupe Espadas-García [ctb, dtc] , Dr. Elisa Monzón-Casanova [ctb, fnd] , Prof. Dr. Eduard Sabidó-Aguade [res, ctb, dtc, fnd]
Maintainer: Aitor Moruno-Cuenca <morunoaitor at gmail.com>
Citation
From within R, enter citation("ProteinBatcher"):
Aitor Moruno-Cuenca. ProteinBatcher: An end-to-end proteomics workflow with condition-aware imputation, flexible statistical modelling and interactive visualization. doi:10.18129/B9.bioc.ProteinBatcher, R package version 0.99.7, https://bioconductor.org/packages/ProteinBatcher.
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("ProteinBatcher")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 0.99.7 |
| License | MIT + file LICENSE |
| URL | https://github.com/DataScienceRD-Almirall/ProteinBatcher |
| Bug Reports | https://github.com/DataScienceRD-Almirall/ProteinBatcher/issues |
| Last updated | 2026-08-21 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| Downloads rank | 2436 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | BatchEffect, DataImport, DataRepresentation, MassSpectrometry, Proteomics, Software |
| Package Short Url | https://bioconductor.org/packages/ProteinBatcher/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ProteinBatcher")| ProteinBatcher workflow | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | ProteinBatcher_0.99.7.tar.gz |
| Windows binary (x86_64) | ProteinBatcher_0.99.7.zip |
| macOS binary (arm64) | ProteinBatcher_0.99.7.tgz |
| macOS binary (x86_64) | ProteinBatcher_0.99.7.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ProteinBatcher |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ProteinBatcher |
| Package Downloads Report | Download Stats |
Dependencies
Imports: data.table, ggplot2, ggrepel, grDevices, grid, limma, methods, S4Vectors, stats, SummarizedExperiment, utils
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)