Package: squallms
Type: Package
Title: Speedy quality assurance via lasso labeling for LC-MS data
Version: 1.4.0
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 (>= 4.1.0)
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
Config/pak/sysreqs: libglpk-dev make libicu-dev libxml2-dev
        libnetcdf-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:30:51 UTC
RemoteUrl: https://github.com/bioc/squallms
RemoteRef: RELEASE_3_22
RemoteSha: b2083b7a4fda2fbeb8a64da05b26cf346a2b2721
NeedsCompilation: no
Packaged: 2026-03-05 08:03:27 UTC; root
Author: William Kumler [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-5022-8009>)
Maintainer: William Kumler <wkumler@uw.edu>
Built: R 4.5.2; ; 2026-03-05 08:06:01 UTC; windows
