Package: proBatch
Type: Package
Title: Tools for Diagnostics and Corrections of Batch Effects in
        Proteomics
Version: 2.1.3
Authors@R: c(
    person("Jelena", "Cuklina", email = "chuklina.jelena@gmail.com", role = "aut"),
    person("Chloe H.", "Lee", email = "chloe.h.lee94@gmail.com", role = "aut"),
    person("Patrick", "Pedrioli", email = "pedrioli@gmail.com", role = "aut"),
    person("Olga", "Zolotareva", email = "olga.zolotareva@uni-hamburg.de", role = "aut"),
    person("Yuliya", "Burankova", email = "yuliya.burankova@uni-hamburg.de", role = "cre")   
  )
Description: 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.
biocViews: BatchEffect, Normalization, Preprocessing, Software,
        MassSpectrometry, Proteomics, QualityControl, Visualization
License: GPL-3
URL: https://github.com/Freddsle/proBatch
BugReports: https://github.com/Freddsle/proBatch/issues
Depends: R (>= 4.5.0)
Encoding: UTF-8
LazyData: false
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
VignetteBuilder: knitr
Language: en-US
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-08-01 16:27:55 UTC
RemoteUrl: https://github.com/bioc/proBatch
RemoteRef: HEAD
RemoteSha: c7624a207aeb778804b52de442de28a0b77af714
NeedsCompilation: no
Packaged: 2026-10-31 10:16:44 UTC; root
Author: Jelena Cuklina [aut],
  Chloe H. Lee [aut],
  Patrick Pedrioli [aut],
  Olga Zolotareva [aut],
  Yuliya Burankova [cre]
Maintainer: Yuliya Burankova <yuliya.burankova@uni-hamburg.de>