Package: gutenTAG
Type: Package
Title: gutenTAG: MALDI-IHC Data Processing and Quality Control
Version: 0.99.14
Authors@R: c(
    person("John", "Abbey", email = "john.abbey@uzh.ch", role = c("aut", "cre")),
    person("Pierre", "Bost", role = "aut"),
    person("Leonardo", "Schwarz", role = "aut")
  )
Description: gutenTAG is an R package for the data processing and quality control of targeted MALDI mass spectrometry imaging (MALDI-MSI) data. It builds on [Cardinal](https://bioconductor.org/packages/Cardinal/), a Bioconductor framework for MSI data, and extends it with targeted workflows specific to MALDI-imaging experiments.The core processing approach uses a novel metapeak construction strategy to account for mass shift and isotopic peaks in the spectra. Downstream, the package provides image-level and spatial quality control statistics, and supports conversion to standard Bioconductor formats such as `SpatialExperiment`, `CytoImageList`, and `AnnData` — enabling dimensionality reduction, clustering, and visualisation using the broader Bioconductor ecosystem. Image visualisation is supported through [cytomapper](https://bioconductor.org/packages/cytomapper/) and [cytoviewer](https://bioconductor.org/packages/cytoviewer/), a Shiny-based interactive viewer for CytoImageList objects that enables interactive exploration of multichannel images.
Depends: R (>= 4.1.0), Cardinal (>= 3.6.2)
Imports: ggplot2, ProtGenerics, dplyr, stats, methods, mclust, splus2R,
        abind, cytomapper, EBImage, Matrix, utils, matter,
        SpatialExperiment, BiocParallel, flexmix, ggrepel, rlang
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.3
Suggests: anndata, BiocStyle, knitr, rmarkdown, markdown, reticulate,
        testthat (>= 3.0.0), plotly, sessioninfo, quarto
biocViews: ImagingMassSpectrometry, Spatial, Proteomics
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-04-23 14:54:54 UTC; pkgbuild
Author: John Abbey [aut, cre],
  Pierre Bost [aut],
  Leonardo Schwarz [aut]
Maintainer: John Abbey <john.abbey@uzh.ch>
