ProteinBatcher

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.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ProteinBatcher")