DOI: 10.18129/B9.bioc.proBatch  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see proBatch.

Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Bioconductor version: 3.16

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>

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PDF R Script proBatch package overview
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biocViews BatchEffect, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, Software
Version 1.14.0
In Bioconductor since BioC 3.9 (R-3.6) (4 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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