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  "Title": "Spatial Metabolomics and Multi-Omics Analysis",
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      "title": "Convert a binned Cardinal matrix to an optional Seurat object",
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        "binnedCardinalToSeurat"
      ]
    },
    {
      "page": "binSpaMTP",
      "title": "Bin aligned spatial metabolomics features",
      "topics": [
        "binSpaMTP",
        "binSpaMTP,ANY-method",
        "binSpaMTP,MSImagingArrays-method",
        "binSpaMTP,MSImagingExperiment-method",
        "binSpaMTP,SpatialExperiment-method"
      ]
    },
    {
      "page": "buildGeneMappingIndex",
      "title": "Build a gene identity index from RaMP and HGNC",
      "topics": [
        "buildGeneMappingIndex"
      ]
    },
    {
      "page": "buildMZAnnotationIndex",
      "title": "Build a reusable indexed metabolite annotation search space",
      "topics": [
        "buildMZAnnotationIndex"
      ]
    },
    {
      "page": "buildPathwayIndex",
      "title": "Build a shared, auditable pathway membership index",
      "topics": [
        "buildPathwayIndex"
      ]
    },
    {
      "page": "calculate_bounds",
      "title": "Calculates the mz range of the observed_df",
      "topics": [
        "calculate_bounds"
      ]
    },
    {
      "page": "calculateAnnotationStatistics",
      "title": "Rank annotations for all MSI features",
      "topics": [
        "calculateAnnotationStatistics"
      ]
    },
    {
      "page": "calculateSingleAnnotationStatistics",
      "title": "Rank candidate metabolite annotations using paired pathway expression",
      "topics": [
        "calculateSingleAnnotationStatistics"
      ]
    },
    {
      "page": "cardinalToSeurat",
      "title": "Convert a Cardinal object to an optional Seurat object",
      "topics": [
        "cardinalToSeurat"
      ]
    },
    {
      "page": "cardinalToSpatialExperiment",
      "title": "Convert an aligned Cardinal experiment to SpatialExperiment",
      "topics": [
        "cardinalToSpatialExperiment"
      ]
    },
    {
      "page": "check_and_truncate_adduct_vector",
      "title": "Checks if the complete adduct is in the data base, else returns a truncated adduct",
      "topics": [
        "check_and_truncate_adduct_vector"
      ]
    },
    {
      "page": "check_cardinal_version",
      "title": "Check Cardinal Version",
      "topics": [
        "check_cardinal_version"
      ]
    },
    {
      "page": "checkAlignment",
      "title": "Inspect the alignment of two spatial experiments",
      "topics": [
        "checkAlignment"
      ]
    },
    {
      "page": "combineTransformations",
      "title": "Combines rigid tranformation matrices",
      "topics": [
        "combineTransformations"
      ]
    },
    {
      "page": "convertSeuratToCardinal",
      "title": "Convert an optional Seurat object to Cardinal",
      "topics": [
        "convertSeuratToCardinal"
      ]
    },
    {
      "page": "createMergedModalityAssay",
      "title": "Combine paired modalities in a scaled alternative experiment",
      "topics": [
        "createMergedModalityAssay"
      ]
    },
    {
      "page": "createPathwayAssay",
      "title": "Create a RaMP identity alternative experiment",
      "topics": [
        "createPathwayAssay"
      ]
    },
    {
      "page": "createPathwayObject",
      "title": "Store pathway scores in an alternative experiment",
      "topics": [
        "createPathwayObject"
      ]
    },
    {
      "page": "db_adduct_filter",
      "title": "Filters the provided metabolomic database by polarity and adducts",
      "topics": [
        "db_adduct_filter"
      ]
    },
    {
      "page": "deconvolveSMILES",
      "title": "Decompose explicit functional groups in SMILES strings",
      "topics": [
        "deconvolveSMILES"
      ]
    },
    {
      "page": "demsHeatmap",
      "title": "Heatmap of Differentially Expressed Metabolites",
      "topics": [
        "demsHeatmap"
      ]
    },
    {
      "page": "densityMap",
      "title": "Export an interactive spatial detection-density viewer",
      "topics": [
        "densityMap"
      ]
    },
    {
      "page": "experimentAccess",
      "title": "Access SpaMTP data through Bioconductor containers",
      "topics": [
        "experimentAccess"
      ]
    },
    {
      "page": "findAllDEMs",
      "title": "Finds differentially expressed m/z values/metabolites between all comparison groups.",
      "topics": [
        "findAllDEMs"
      ]
    },
    {
      "page": "findCorrelatedFeatures",
      "title": "Find features correlated with a metabolite, gene, or pixel group",
      "topics": [
        "findCorrelatedFeatures"
      ]
    },
    {
      "page": "findDuplicateAnnotations",
      "title": "Finds if any metabolite is duplicated across multiple m/z values.",
      "topics": [
        "findDuplicateAnnotations"
      ]
    },
    {
      "page": "findNearestMZ",
      "title": "Finds the nearest m/z peak to a given value in a SpaMTP Object",
      "topics": [
        "findNearestMZ"
      ]
    },
    {
      "page": "findRegionalPathways",
      "title": "Regional Pathway Enrichment",
      "topics": [
        "findRegionalPathways"
      ]
    },
    {
      "page": "findSpatiallyVariableMetabolites",
      "title": "Find spatially variable metabolites using Moran's I",
      "topics": [
        "findSpatiallyVariableMetabolites"
      ]
    },
    {
      "page": "fishersPathwayAnalysis",
      "title": "Fisher Exact Tests for Pathway Enrichment",
      "topics": [
        "fishersPathwayAnalysis"
      ]
    },
    {
      "page": "formula_filter",
      "title": "Filters reference Database to only select natural elements",
      "topics": [
        "formula_filter"
      ]
    },
    {
      "page": "get_analytes_db",
      "title": "Helper function for building a pathway db based on detected",
      "topics": [
        "get_analytes_db"
      ]
    },
    {
      "page": "getKmeanClusters",
      "title": "Perform K-means clustering on a specified reduction",
      "topics": [
        "getKmeanClusters"
      ]
    },
    {
      "page": "getMetaspace",
      "title": "Core METASPACE Data Retrieval",
      "topics": [
        "getMetaspace"
      ]
    },
    {
      "page": "getMZMetadata",
      "title": "Gets values from a single metadata column for a respective m/z value.",
      "topics": [
        "getMZMetadata"
      ]
    },
    {
      "page": "getRefinedAnnotations",
      "title": "Refines and reduces m/z annotations",
      "topics": [
        "getRefinedAnnotations"
      ]
    },
    {
      "page": "getSpatiallyVariableMetabolites",
      "title": "Get the top spatially variable metabolites",
      "topics": [
        "getSpatiallyVariableMetabolites"
      ]
    },
    {
      "page": "getSquareCoordinates",
      "title": "This function computes the coordinates of a square's four corners based on a given center point and width.",
      "topics": [
        "getSquareCoordinates"
      ]
    },
    {
      "page": "imageMZAnnotationPlot",
      "title": "Plot annotated metabolites without an optical image",
      "topics": [
        "imageMZAnnotationPlot"
      ]
    },
    {
      "page": "imageMZPlot",
      "title": "Plot MSI features from a Bioconductor spatial container",
      "topics": [
        "imageMZPlot"
      ]
    },
    {
      "page": "interactiveSpatialPlot",
      "title": "Interactively inspect mass windows in a spatial experiment",
      "topics": [
        "interactiveSpatialPlot"
      ]
    },
    {
      "page": "kNeighborsGraph",
      "title": "Construct a k-Nearest Neighbour Graph from Spatial Coordinates.",
      "topics": [
        "kNeighborsGraph"
      ]
    },
    {
      "page": "labels_to_show",
      "title": "Filters the annotation list to only include the first n number of annotations per m/z",
      "topics": [
        "labels_to_show"
      ]
    },
    {
      "page": "loadMetaspace",
      "title": "Load METASPACE Data as a SpatialExperiment",
      "topics": [
        "loadMetaspace"
      ]
    },
    {
      "page": "loadSM",
      "title": "Load imzML data into a Bioconductor-native spatial container",
      "topics": [
        "loadSM"
      ]
    },
    {
      "page": "loadSpaMTPDatabase",
      "title": "Load versioned SpaMTP annotation resources",
      "topics": [
        "loadSpaMTPDatabase"
      ]
    },
    {
      "page": "maldiMatrixProfiles",
      "title": "List MALDI matrix and on-tissue derivatization profiles",
      "topics": [
        "maldiMatrixProfiles"
      ]
    },
    {
      "page": "maldiMatrixRules",
      "title": "Select annotation rules from the MALDI matrix/reagent profile",
      "topics": [
        "maldiMatrixRules"
      ]
    },
    {
      "page": "mapGeneIdentifiers",
      "title": "Map gene identifiers with an auditable HGNC identity",
      "topics": [
        "mapGeneIdentifiers"
      ]
    },
    {
      "page": "mapSpatialOmics",
      "title": "Map metabolite intensities to transcriptomic pixels or cells",
      "topics": [
        "mapSpatialOmics"
      ]
    },
    {
      "page": "massIntensityPlot",
      "title": "Plot mean mass spectra from a native spatial experiment",
      "topics": [
        "massIntensityPlot"
      ]
    },
    {
      "page": "metaspaceClient",
      "title": "Metaspace R Client Constructor",
      "topics": [
        "metaspaceClient"
      ]
    },
    {
      "page": "metaspaceToFeatureMatrix",
      "title": "Convert METASPACE Images to Feature Matrix",
      "topics": [
        "metaspaceToFeatureMatrix"
      ]
    },
    {
      "page": "multiOmicIntegration",
      "title": "Integrate paired modalities using native PCA embeddings",
      "topics": [
        "multiOmicIntegration",
        "multiOmicIntegration,ANY-method",
        "multiOmicIntegration,SpatialExperiment-method"
      ]
    },
    {
      "page": "mzBoxPlot",
      "title": "Generates a Boxplot of spatial metabolic intensity data",
      "topics": [
        "mzBoxPlot"
      ]
    },
    {
      "page": "mzRidgePlot",
      "title": "Generates a ridge plot of spatial metabolic intensity data",
      "topics": [
        "mzRidgePlot"
      ]
    },
    {
      "page": "mzViolinPlot",
      "title": "Generates a violin plot of spatial metabolic intensity data",
      "topics": [
        "mzViolinPlot"
      ]
    },
    {
      "page": "normalizeSMData",
      "title": "Normalize spatial metabolomics intensity data",
      "topics": [
        "normalizeSMData",
        "normalizeSMData,ANY-method",
        "normalizeSMData,MSImagingArrays-method",
        "normalizeSMData,MSImagingExperiment-method",
        "normalizeSMData,SingleCellExperiment-method"
      ]
    },
    {
      "page": "pathwayNetworkPlots",
      "title": "Construct an interactive pathway network visualization",
      "topics": [
        "pathwayNetworkPlots"
      ]
    },
    {
      "page": "pixelPlot",
      "title": "Convert point symbols to squares without changing coordinates or scales",
      "topics": [
        "pixelPlot"
      ]
    },
    {
      "page": "plot3DFeature",
      "title": "Compare two spatial features in 3D",
      "topics": [
        "plot3DFeature"
      ]
    },
    {
      "page": "plotPathways",
      "title": "Plot named pathways on a dimensionality reduction",
      "topics": [
        "plotPathways"
      ]
    },
    {
      "page": "plotPathwaysSpatially",
      "title": "Plot named pathways in tissue coordinates",
      "topics": [
        "plotPathwaysSpatially"
      ]
    },
    {
      "page": "plotRegionalPathways",
      "title": "Plot significantly enriched pathways per region",
      "topics": [
        "plotRegionalPathways"
      ]
    },
    {
      "page": "plotSinglePathway",
      "title": "Plot a pathway score on a Bioconductor dimensionality reduction",
      "topics": [
        "plotSinglePathway"
      ]
    },
    {
      "page": "plotSinglePathwaySpatially",
      "title": "Plot a pathway score in tissue coordinates",
      "topics": [
        "plotSinglePathwaySpatially"
      ]
    },
    {
      "page": "plotSpatialFeature",
      "title": "Plot spatial features from a Bioconductor container",
      "topics": [
        "plotSpatialFeature",
        "plotSpatialFeature,MSImagingExperiment-method",
        "plotSpatialFeature,SpatialExperiment-method"
      ]
    },
    {
      "page": "ppm_error",
      "title": "Calculates the ppm error as a valve",
      "topics": [
        "ppm_error"
      ]
    },
    {
      "page": "ppm_range_match",
      "title": "Check whether m/z values match within a ppm tolerance",
      "topics": [
        "ppm_range_match"
      ]
    },
    {
      "page": "predictAdductsFromSMILES",
      "title": "Predict a structure-aware adduct search space from SMILES",
      "topics": [
        "predictAdductsFromSMILES"
      ]
    },
    {
      "page": "print.spamtp_mz_index",
      "title": "Print an indexed metabolite annotation search space",
      "topics": [
        "print.spamtp_mz_index"
      ]
    },
    {
      "page": "Pseudo_msms",
      "title": "Find all library spectra10 above a cosine threshold for each imaging peak, restricting to a global precursor-mz range.",
      "topics": [
        "Pseudo_msms"
      ]
    },
    {
      "page": "queryMZAnnotationIndex",
      "title": "Query an indexed metabolite annotation search space",
      "topics": [
        "queryMZAnnotationIndex"
      ]
    },
    {
      "page": "reaction_type",
      "title": "Pathway-network reaction styles",
      "topics": [
        "reaction_type"
      ]
    },
    {
      "page": "readSMMatrix",
      "title": "Read a binned spatial metabolomics matrix",
      "topics": [
        "readSMMatrix"
      ]
    },
    {
      "page": "refineLipids",
      "title": "Uses common lipid nomenclature to simplify lipid annotations",
      "topics": [
        "refineLipids"
      ]
    },
    {
      "page": "renderSpaMTPReport",
      "title": "Render a portable, self-contained multi-omics report",
      "topics": [
        "renderSpaMTPReport"
      ]
    },
    {
      "page": "runDE",
      "title": "Run limma contrasts on log-transformed technical pools",
      "topics": [
        "runDE"
      ]
    },
    {
      "page": "runMetabolicPCA",
      "title": "Compute PCA with scater on a selected experiment",
      "topics": [
        "runMetabolicPCA"
      ]
    },
    {
      "page": "runPooling",
      "title": "Pools Bioconductor experiment into random pools for pseudo-bulking.",
      "topics": [
        "runPooling"
      ]
    },
    {
      "page": "runRAMPGeseca",
      "title": "Runs multilevel Monte-Carlo variant for performing gene sets co-regulation analysis using the RAMP_DB metabolite/gene database.",
      "topics": [
        "runRAMPGeseca"
      ]
    },
    {
      "page": "runSpaMTPWorkflow",
      "title": "Run a reproducible spatial multi-omics workflow and HTML report",
      "topics": [
        "runSpaMTPWorkflow"
      ]
    },
    {
      "page": "runSpatialGraphPCA",
      "title": "Perform Dimensionality Reduction using Graph-Regularised PCA on Spatial Data",
      "topics": [
        "runSpatialGraphPCA"
      ]
    },
    {
      "page": "savePheatmapAsPDF",
      "title": "Saves a demsHeatmap as a PDF",
      "topics": [
        "savePheatmapAsPDF"
      ]
    },
    {
      "page": "saveSpaMTPData",
      "title": "Export an experiment's expression matrix and metadata",
      "topics": [
        "saveSpaMTPData"
      ]
    },
    {
      "page": "scaleSMData",
      "title": "Centre and scale features within a Bioconductor experiment",
      "topics": [
        "scaleSMData"
      ]
    },
    {
      "page": "searchAnnotations",
      "title": "Find Annotation",
      "topics": [
        "searchAnnotations"
      ]
    },
    {
      "page": "selectROIs",
      "title": "Launch an Interactive ROI Annotation App for SpatialExperiment",
      "topics": [
        "selectROIs"
      ]
    },
    {
      "page": "seuratToSingleCellExperiment",
      "title": "Convert Seurat expression data to SingleCellExperiment",
      "topics": [
        "seuratToSingleCellExperiment"
      ]
    },
    {
      "page": "seuratToSpatialExperiment",
      "title": "Convert a Seurat object to SpatialExperiment",
      "topics": [
        "seuratToSpatialExperiment"
      ]
    },
    {
      "page": "spaMTPDatabaseInfo",
      "title": "Inspect SpaMTP database resources",
      "topics": [
        "spaMTPDatabaseInfo"
      ]
    },
    {
      "page": "spatialExperimentToCardinal",
      "title": "Convert a SpatialExperiment to Cardinal",
      "topics": [
        "spatialExperimentToCardinal"
      ]
    },
    {
      "page": "spatialExperimentToSeurat",
      "title": "Convert a SpatialExperiment to an optional Seurat object",
      "topics": [
        "spatialExperimentToSeurat"
      ]
    },
    {
      "page": "spatialMZAnnotationPlot",
      "title": "Plot annotated metabolites with optional optical images",
      "topics": [
        "spatialMZAnnotationPlot"
      ]
    },
    {
      "page": "spatialMZPlot",
      "title": "Plot MSI features with optional optical images",
      "topics": [
        "spatialMZPlot"
      ]
    },
    {
      "page": "spectralBinning",
      "title": "Spectral binning of intensity values stored in a Matrix object, converted from matter.",
      "topics": [
        "spectralBinning"
      ]
    },
    {
      "page": "statPlot",
      "title": "Helper function for QC plots by generating intensity count data",
      "topics": [
        "statPlot"
      ]
    },
    {
      "page": "subsetMZFeatures",
      "title": "Subset a Bioconductor experiment by a list of m/z's",
      "topics": [
        "subsetMZFeatures"
      ]
    },
    {
      "page": "subsetSPM",
      "title": "Subset features and pixels through Bioconductor containers",
      "topics": [
        "subsetSPM"
      ]
    },
    {
      "page": "tmmNormalize",
      "title": "Performs TMM normalization between categories based on a specified ident",
      "topics": [
        "tmmNormalize"
      ]
    },
    {
      "page": "vignetteData",
      "title": "Small real spatial experiments for the vignettes",
      "topics": [
        "vignetteData"
      ]
    },
    {
      "page": "visualisePathways",
      "title": "Visualise Significant Pathways",
      "topics": [
        "visualisePathways"
      ]
    }
  ],
  "_pkglogo": "https://github.com/BiocStaging/SpaMTP/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/BiocStaging/SpaMTP/raw/HEAD/README.md",
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  "_vignettes": [
    {
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