Package: ProteinBatcher
Title: An end-to-end proteomics workflow with condition-aware
        imputation, flexible statistical modelling and interactive
        visualization
Version: 0.99.7
Authors@R: 
    c(person(given = "Aitor", family ="Moruno-Cuenca", email = "morunoaitor@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0009-0009-8133-2552")),
    person(given = "Dr. Sergi", family = "Sayols-Puig", email = "sergi.sayolspuig@almirall.com", role = c("ctb"), comment = c(ORCID = "0000-0002-3877-4170")),
    person(given = "Dr. Bruna", family = "Oriol-Tordera", email = "bruna.orioltordera@almirall.com", role = c("ctb"), comment = c(ORCID = "0000-0002-2714-9097")),
    person(given = "Dr. Hiba", family = "Salim", email = "hiba.salim@crg.eu", role = c("dtc"), comment = c(ORCID = "0000-0002-2168-0258")),
    person(given = "Dr. Francesc", family = "Fernández-Albert", email = "francesc.fernandez@almirall.com", role = c("ths"), comment = c(ORCID = "0000-0001-5561-0701")),
    person(given = "Prof. Dr. Alexandre", family = "Perera-Lluna", email = "alexandre.perera@upc.edu", role = c("ths"), comment = c(ORCID = "0000-0001-6427-851X")),
    person(given = "Dr. Guadalupe", family = "Espadas-García", email = "guadalupe.espadas@crg.eu", role = c("ctb", "dtc"), comment = c(ORCID = "0000-0002-6415-8013")),
    person(given = "Dr. Elisa", family = "Monzón-Casanova", email = "elisa.monzoncasanova@almirall.com", role = c("ctb", "fnd"), comment = c(ORCID = "0000-0001-6617-6138")),
    person(given = "Prof. Dr. Eduard", family = "Sabidó-Aguade", email = "eduard.sabido@upf.edu", role = c("res", "ctb", "dtc", "fnd"), comment = c(ORCID = "0000-0001-6506-7714")))
Description: 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.
License: MIT + file LICENSE
URL: https://github.com/DataScienceRD-Almirall/ProteinBatcher
BugReports: https://github.com/DataScienceRD-Almirall/ProteinBatcher/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Imports: data.table, ggplot2, ggrepel, grDevices, grid, limma, methods,
        S4Vectors, stats, SummarizedExperiment, utils
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
biocViews: Proteomics, MassSpectrometry, DataImport,
        DataRepresentation, Software, BatchEffect
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-08-21 16:59:35 UTC
RemoteUrl: https://github.com/bioc/ProteinBatcher
RemoteRef: HEAD
RemoteSha: 1c6df35e6b9a0f0f333f23521ff00b7bd5ff508f
NeedsCompilation: no
Packaged: 2026-10-11 10:32:28 UTC; root
Author: Aitor Moruno-Cuenca [aut, cre] (ORCID:
    <https://orcid.org/0009-0009-8133-2552>),
  Dr. Sergi Sayols-Puig [ctb] (ORCID:
    <https://orcid.org/0000-0002-3877-4170>),
  Dr. Bruna Oriol-Tordera [ctb] (ORCID:
    <https://orcid.org/0000-0002-2714-9097>),
  Dr. Hiba Salim [dtc] (ORCID: <https://orcid.org/0000-0002-2168-0258>),
  Dr. Francesc Fernández-Albert [ths] (ORCID:
    <https://orcid.org/0000-0001-5561-0701>),
  Prof. Dr. Alexandre Perera-Lluna [ths] (ORCID:
    <https://orcid.org/0000-0001-6427-851X>),
  Dr. Guadalupe Espadas-García [ctb, dtc] (ORCID:
    <https://orcid.org/0000-0002-6415-8013>),
  Dr. Elisa Monzón-Casanova [ctb, fnd] (ORCID:
    <https://orcid.org/0000-0001-6617-6138>),
  Prof. Dr. Eduard Sabidó-Aguade [res, ctb, dtc, fnd] (ORCID:
    <https://orcid.org/0000-0001-6506-7714>)
Maintainer: Aitor Moruno-Cuenca <morunoaitor@gmail.com>