gutenTAG

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.

Code

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Topics

People

• John Abbey author maintainer
• Pierre Bost author
• Leonardo Schwarz author