Package: QFeatures
Title: Quantitative features for mass spectrometry data
Version: 1.23.1
Authors@R: c(person("Laurent", "Gatto",
                    email = "laurent.gatto@uclouvain.be",
                    comment = c(ORCID = "0000-0002-1520-2268"),
                    role = c("aut", "cre")),
             person("Christophe", "Vanderaa",
                    email = "christophe.vanderaa@uclouvain.be",
                    comment = c(ORCID = "0000-0001-7443-5427"),
                    role = "aut"),
             person("Karolína", "Kryštofová",
                    comment = c(ORCID = "0009-0004-2896-2188"),
                    role = "ctb"),
             person("Léopold", "Guyot",
                     email = "leopold.guyot@uclouvain.be",
                     role = "ctb"))
Description: The QFeatures infrastructure enables the management and
        processing of quantitative features for high-throughput mass
        spectrometry assays. It provides a familiar Bioconductor user
        experience to manages quantitative data across different assay
        levels (such as peptide spectrum matches, peptides and
        proteins) in a coherent and tractable format.
Depends: R (>= 4.1), MultiAssayExperiment (>= 1.33.6)
Imports: methods, stats, utils, S4Vectors, IRanges,
        SummarizedExperiment, BiocGenerics (>= 0.53.4), ProtGenerics
        (>= 1.35.1), AnnotationFilter, lazyeval, Biobase, MsCoreUtils
        (>= 1.25.3), igraph, grDevices, plotly, tidyr, dplyr,
        tidyselect, reshape2
Suggests: SingleCellExperiment, MsDataHub (>= 1.11.5), arrow, Matrix,
        HDF5Array, ggplot2, gplots, limma, DT, shiny, shinydashboard,
        testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore,
        matrixStats, imputeLCMD, pcaMethods, impute, norm,
        ComplexHeatmap
biocViews: Infrastructure, MassSpectrometry, Proteomics, Metabolomics
License: Artistic-2.0
Encoding: UTF-8
VignetteBuilder: knitr
BugReports: https://github.com/rformassspectrometry/QFeatures/issues
URL: https://rformassspectrometry.github.io/QFeatures
Collate: 'AllGenerics.R' 'AssayLinks.R' 'QFeatures-class.R'
        'QFeatures-functions.R' 'QFeatures-longForm.R'
        'QFeatures-processing.R' 'QFeatures-filter.R'
        'QFeatures-missing-data.R' 'QFeatures-aggregation.R'
        'QFeatures-imputation.R' 'QFeatures-join.R'
        'QFeatures-validity.R' 'SummarizedExperiment-methods.R'
        'subsetBy-methods.R' 'readQFeatures.R'
        'readQFeaturesFromDIANN.R' 'data.R' 'reduce.R' 'utils.R'
        'display.R'
Roxygen: list(markdown=TRUE)
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-03 15:27:22 UTC
RemoteUrl: https://github.com/bioc/QFeatures
RemoteRef: HEAD
RemoteSha: b4667576ef2fbdb199ee1e0c521e1f4c1609f56d
NeedsCompilation: no
Packaged: 2026-07-02 06:00:31 UTC; root
Author: Laurent Gatto [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1520-2268>),
  Christophe Vanderaa [aut] (ORCID:
    <https://orcid.org/0000-0001-7443-5427>),
  Karolína Kryštofová [ctb] (ORCID:
    <https://orcid.org/0009-0004-2896-2188>),
  Léopold Guyot [ctb]
Maintainer: Laurent Gatto <laurent.gatto@uclouvain.be>