Package: prolfqua
Type: Package
Title: Proteomics Label Free Quantification
Version: 0.99.3
Authors@R: c(
    person("Witold", "Wolski",
        email = "witold.wolski@fgcz.uzh.ch",
        role = "aut",
        comment = c(ORCID = "0000-0002-6468-120X")),
    person("Functional Genomics Center Zurich",
        role = "fnd"),
    person("Christian", "Panse",
        email = "cp@fgcz.ethz.ch",
        role = "cre",
        comment = c(ORCID = "0000-0003-1975-3064")))
Description: The prolfqua package integrates essential steps of the
        mass spectrometry based label free quantification data analysis
        workflow: quality control, data normalization, protein
        aggregation, modeling, hypothesis testing and sample size
        estimation. We use prolfqua to : develop highly customizable,
        visually appealing, and interactive data analysis reports in
        pdf or HTML format; to visualize and model simple experimental
        designs with a single explanatory variable and complex
        experiments with multiple factors; to benchmark data
        acquisition, data preprocessing or data modeling methods. We
        developed and improved the package by applying the "Eating your
        own dog food" principle, when analysing dozens of proteomics
        datasets.
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://github.com/fgcz/prolfqua, https://fgcz.github.io/prolfqua/
BugReports: https://github.com/fgcz/prolfqua/issues
Imports: circlize, ComplexHeatmap, dplyr, forcats, ggplot2, ggbeeswarm,
        ggrepel, limma, lme4, lmerTest, logistf, MASS, methods, plotly,
        progress, purrr, rlang, stringi, tidyselect, tidyr, tibble,
        UpSetR, withr
Suggests: BiocCheck, BiocStyle, corrplot, covr, crosstalk, cyclocomp,
        devtools, goodpractice, gridExtra, KernSmooth, knitr, limpa,
        lintr, pkgdown, preprocessCore, rcmdcheck, Rfit, rmarkdown,
        roxygen2, S4Vectors, SummarizedExperiment, testthat, vsn
RoxygenNote: 7.3.3
Roxygen: list(r6 = TRUE)
Depends: R (>= 4.5)
biocViews: MassSpectrometry, Proteomics, Metabolomics, Normalization,
        Preprocessing, QualityControl
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libuv1-dev
        libssl-dev perl libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-23 08:07:47 UTC
RemoteUrl: https://github.com/bioc/prolfqua
RemoteRef: HEAD
RemoteSha: 0726bc3c1001b999013bee2174ba3a46dd90edb9
NeedsCompilation: no
Packaged: 2026-10-23 13:47:51 UTC; root
Author: Witold Wolski [aut] (ORCID: <https://orcid.org/0000-0002-6468-120X>),
  Functional Genomics Center Zurich [fnd],
  Christian Panse [cre] (ORCID: <https://orcid.org/0000-0003-1975-3064>)
Maintainer: Christian Panse <cp@fgcz.ethz.ch>