Package: squallms
Type: Package
Title: Speedy quality assurance via lasso labeling for LC-MS data
Version: 1.5.0
Authors@R: c(
  person(given = "William", family = "Kumler", email = "wkumler@uw.edu",
         role = c("aut", "cre", "cph"), comment=c(ORCID="0000-0002-5022-8009"))
  )
Description: squallms is a Bioconductor R package that implements a 
  "semi-labeled" approach to untargeted mass spectrometry data. It pulls in raw 
  data from mass-spec files to calculate several metrics that are then used to 
  label MS features in bulk as high or low quality. These metrics of peak quality
  are then passed to a simple logistic model that produces a fully-labeled 
  dataset suitable for downstream analysis. 
License: MIT + file LICENSE
URL: https://github.com/wkumler/squallms
BugReports: https://github.com/wkumler/squallms/issues
Encoding: UTF-8
RoxygenNote: 7.3.1
biocViews: MassSpectrometry, Metabolomics, Proteomics, Lipidomics, ShinyApps,
  Classification, Clustering, FeatureExtraction, PrincipalComponent, Regression,
  Preprocessing, QualityControl, Visualization
Depends:
    R (>= 3.5.0)
Imports:
    xcms,
    MSnbase,
    MsExperiment,
    RaMS,
    dplyr,
    tidyr,
    tibble,
    ggplot2,
    shiny,
    plotly,
    data.table,
    caret,
    stats,
    graphics,
    utils,
    keys
Suggests:
    knitr,
    rmarkdown,
    BiocStyle,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/squallms
git_branch: devel
git_last_commit: 26f2e18
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
