quantMSImageR - Processing and Quantification of Targeted Mass Spectrometry Imaging Data
Implements tools for processing and quantifying targeted DESI-MRM mass spectrometry imaging (MSI) datasets, extending the Cardinal package. Includes signal-to-noise filtering against background pixels, tissue/background separation, per-feature ion images, quantile heatmaps, quantification against on-slide or on-tissue calibration standards, and batch export of per-feature text images for external viewers.
Last updated
softwaremassspectrometryimagingmassspectrometrymetabolomicslipidomicsqualitycontrolnormalizationvisualization
5.00 score 188 downloads
MRManalyzeR - Process and Analyse Targeted LC-MS Lipidomics and Metabolomics Data
Reproducible post-acquisition processing of targeted LC-MS/MS lipidomics and metabolomics results exported from Waters TargetLynx or from Skyline, or supplied as a plain sample-by-analyte matrix. Reads the quantitative result tables, integrates them with sample and feature metadata, and applies configurable signal filtering (SNR, LOD or LOQ), blank filtering, batch correction, normalisation, internal-standard and volume adjustment of vendor-reported concentrations, and missing-value imputation. Each step is an exported function acting on a struct DatasetExperiment; a complete workflow can additionally be driven from a single YAML configuration via runMRManalyzeR(), which also renders self-contained HTML data-quality and statistical reports. Chromatographic peak detection, peak integration and calibration-curve fitting from raw mass-spectrometry data are outside its scope.
Last updated
metabolomicslipidomicsmassspectrometryqualitycontrolnormalizationbatcheffectvisualizationworkflowstep
2.54 score 6 scripts