Package: ProteinBatcher
Title: Batch Processing and Harmonization of Quantitative Proteomics
        Table
Version: 0.99.0
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
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: assertthat, data.table, dplyr, ggplot2, ggrepel, limma,
        magrittr, methods, S4Vectors, stats, SummarizedExperiment,
        testthat, tibble, tidyr, writexl
Suggests: knitr, rmarkdown, readr, readxl, htmltools
VignetteBuilder: knitr
biocViews: Proteomics, MassSpectrometry, DataImport,
        DataRepresentation, Software, BatchEffect
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-05-04 17:39:44 UTC; pkgbuild
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>
