https://bcrl-tylu.r-universe.devRecent package updates in bcrl-tyluR-universehttps://github.com/bcrl-tylu.pnghttps://bcrl-tylu.r-universe.devWed, 14 Oct 2026 00:22:44 GMTlu.t@wehi.edu.au (Tianyao Lu)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.https://github.com/r-universe/biocstaging/actions/runs/38498957284Wed, 14 Oct 2026 00:22:44 GMTSpaMTP0.99.11successhttps://biocstaging.r-universe.devhttps://github.com/BiocStaging/SpaMTPGene_Identifier_Mapping.RmdGene_Identifier_Mapping.htmlAuditable gene mapping with SpaMTPdb and SpaMTPData2026-09-13 12:19:042026-10-14 00:22:44End_to_End_Workflow.RmdEnd_to_End_Workflow.htmlDesigning and evaluating a spatial multi-omics workflow2026-09-21 01:34:162026-10-14 00:22:44Pathway_Database_Integration.RmdPathway_Database_Integration.htmlPathway databases, interaction provenance, and rebuilding graphs2026-09-21 01:34:162026-09-22 00:11:45SpaMTP_Companion_Workflow.RmdSpaMTP_Companion_Workflow.htmlSpaMTP, SpaMTPdb and SpaMTPData: A Native Companion Workflow2026-09-13 07:38:192026-09-22 00:11:45Metabolite_Annotation_Pipeline.RmdMetabolite_Annotation_Pipeline.htmlSpaMTP: Indexed Metabolite Annotation with RaMP 3.02026-09-13 07:38:192026-10-14 00:22:44Modern_Data_Access.RmdModern_Data_Access.htmlSpaMTP: Modern Data Access and Workflow Migration2026-09-13 07:38:192026-09-22 04:06:42SpaMTP_Bioconductor.RmdSpaMTP_Bioconductor.htmlSpaMTP: Spatial Metabolite Annotation2026-08-14 07:49:302026-09-22 00:11:45lu.t@wehi.edu.au (Tianyao Lu)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.https://github.com/r-universe/bioc/actions/runs/38045849363Sun, 13 Sep 2026 12:18:48 GMTSpaMTPData0.99.5successhttps://bioc.r-universe.devhttps://github.com/bioc/SpaMTPDataSpaMTPData.RmdSpaMTPData.htmlAccessing SpaMTP Experiment Data2026-08-14 02:20:512026-09-13 07:38:11lu.t@wehi.edu.au (Tianyao Lu)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.https://github.com/r-universe/biocstaging/actions/runs/35958492902Sun, 13 Sep 2026 11:34:49 GMTSpaMTPdb0.99.4successhttps://biocstaging.r-universe.devhttps://github.com/BiocStaging/SpaMTPdbSpaMTPdb.RmdSpaMTPdb.htmlAccessing SpaMTP Annotation Resources2026-08-14 02:20:512026-09-13 07:38:02