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SpaMTP - Spatial Metabolomics and Multi-Omics Analysis

Provides analysis, annotation, visualisation, and multi-omic integration methods for spatial metabolomics data. SpaMTP interoperates with Cardinal and SpatialExperiment containers, with optional Seurat conversion; supports indexed accurate-mass annotation using versioned RaMP resources; and implements spatial feature analysis, pathway enrichment, pathway-network visualisation, and alignment with spatial transcriptomics data.

Last updated

massspectrometryimagingmassspectrometrymetabolomicsspatialtranscriptomicsalignment

4.84 score 33 scripts

SpaMTPData - Experiment Data Resources for SpaMTP Workflows

Provides lightweight, version-aware access to spatial metabolomics and multi-omics experiment data used in SpaMTP workflows. Resources cover mouse brain, mouse urinary bladder, simulated single-cell multi-omics, annotation-refinement, and human brain examples. Large files are retrieved through ExperimentHub or verified source-URL caches rather than stored in the package repository. A small deterministic synthetic SpatialExperiment with a paired transcriptome supports offline examples and interoperability tests. Native SpatialExperiment datasets are available in a separate resource release; historical archival objects retain their original representations. Conversion and analysis are handled by the SpaMTP software package. Native experimental files share a Zenodo version family with SpaMTPdb without coupling the packages at runtime.

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experimentdataexperimenthubhomo_sapiens_datamus_musculus_datareproducibleresearchdatapkg

4.00 score 2 scripts

SpaMTPdb - Versioned Annotation Resources for SpaMTP

Provides lightweight, version-aware access to the annotation resources used by SpaMTP. Resources include pruned RaMP chemical, identifier, pathway, and pathway-topology tables, precomputed SMILES functional-group and ionisation features, and legacy metabolite reference tables, plus a separately versioned human gene identifier reference from fixed HGNC archives. RaMP resource files are hosted on Zenodo and described by AnnotationHub metadata rather than bundled in the package. Retrieved files are verified against recorded sizes and checksums and cached for reuse, and a local resource directory can be used for development and reproducible database builds. Maintainer recipes coordinate a shared Zenodo resource collection with SpaMTPData while preserving separate annotation and experiment registries and independent resource versions.

Last updated

annotationdataannotationhub

3.78 score 1 dependents