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    "addVelo",
    "changeUniprot",
    "createCytoSignal",
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    "csToSeurat",
    "findNN",
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    "imputeNicheVelo",
    "imputeVeloLR",
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    "inferNullScoreLR",
    "inferScoreLR",
    "inferSignif",
    "inferVeloLR",
    "mergeCytoSignal",
    "permuteLR",
    "plotCircosNIntr",
    "plotCluster",
    "plotEdge",
    "plotIntrValue",
    "plotNebulaAll",
    "plotNebulaVolcano",
    "plotREVIGO",
    "plotSigCluster",
    "plotSignif",
    "plotVelo",
    "purgeBeforeSave",
    "rankIntrSpatialVar",
    "removeLowQuality",
    "revigo",
    "runNEBULA",
    "runPears.std",
    "SCEToCS",
    "SeuratToCS",
    "show",
    "showCov",
    "showImp",
    "showIntr",
    "showLog",
    "showScore",
    "showUnpt",
    "showVelo",
    "smoothScoreLR",
    "suggestScaleFactor"
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      "table": false,
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      "title": "Interaction database derived from CellphoneDB V2",
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      "class": [
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      "table": true,
      "tojson": true
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      "title": "Interaction database derived from CellphoneDB V2",
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      "class": [
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        "partner_b",
        "protein_name_a",
        "protein_name_b",
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      "page": "dot-inferVeloLR.matrix_like",
      "title": "#' Compute the LR velo for specific ligand-receptor imputation obj pairs #' #' @param object A Cytosignal object #' @param lig.slot The ligand slot to use #' @param recep.slot The receptor slot to use #' @param intr.db.name The intr database name to use #' @param nn.use The neighbor index as niche #' #' @return A Cytosignal object #' @export #' inferVeloLR <- function( object, ... ) UseMethod(generic = 'inferVeloLR', object = object)",
      "topics": [
        ".inferVeloLR.matrix_like"
      ]
    },
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      "page": "Extract.mergedCytoSignal",
      "title": "Extract metadata variable from mergedCytoSignal object",
      "topics": [
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        "$<-.mergedCytoSignal"
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    },
    {
      "page": "addIntrDB",
      "title": "Add interaction database to CytoSignal object",
      "topics": [
        "addIntrDB"
      ]
    },
    {
      "page": "addVelo",
      "title": "Add velocity data to CytoSignal object",
      "topics": [
        "addVelo"
      ]
    },
    {
      "page": "changeUniprot",
      "title": "Subset gene expression matrix according to availability in the UNIPROT database.",
      "topics": [
        "changeUniprot",
        "changeUniprot.CytoSignal",
        "changeUniprot.matrix_like"
      ]
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      "title": "Create a CytoSignal object",
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      ]
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      "title": "Conversion between CytoSignal object and AnnData object in H5AD file",
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        "H5ADToCS"
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    },
    {
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      "title": "Conversion between CytoSignal object and SingleCellExperiment object",
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        "csToSCE",
        "SCEToCS"
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    },
    {
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      "topics": [
        "csToSeurat",
        "SeuratToCS"
      ]
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      "title": "The CytoSignal Class",
      "topics": [
        "CytoSignal",
        "CytoSignal-class"
      ]
    },
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      "title": "Interaction database derived from CellphoneDB V2",
      "topics": [
        "db.cont",
        "db.diff",
        "g_to_u",
        "inter.index"
      ]
    },
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      "page": "dim.mergedCytoSignal",
      "title": "dim Method for mergedCytoSignal object",
      "topics": [
        "dim.mergedCytoSignal"
      ]
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    {
      "page": "findNN",
      "title": "Identify nearest neighbors for each location using different strategies for different types of interactions",
      "topics": [
        "findNN"
      ]
    },
    {
      "page": "findNNDT",
      "title": "Find the direct connected neighbor of each cell, using Delaunay triangulation",
      "topics": [
        "findNNDT"
      ]
    },
    {
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      "title": "Find the neighbors of each cell in the Epsilon Ball",
      "topics": [
        "findNNGauEB"
      ]
    },
    {
      "page": "findNNRaw",
      "title": "Create a ImpData object using raw data without imputation",
      "topics": [
        "findNNRaw"
      ]
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      "page": "format.CytosignalIntrDEG",
      "title": "Format a CytosignalIntrDEG object to string",
      "topics": [
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    },
    {
      "page": "formatLRDB",
      "title": "Process Ligand–Receptor Data Without Assigning New Random CPI-CC IDs",
      "topics": [
        "formatLRDB"
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    },
    {
      "page": "graphNicheLR",
      "title": "Compute the LR score for specific ligand-receptor imputation obj pairs",
      "topics": [
        "graphNicheLR"
      ]
    },
    {
      "page": "graphNicheLR.CytoSignal",
      "title": "Sub function for graphNicheLR, input a CytoSignal object",
      "topics": [
        "graphNicheLR.CytoSignal"
      ]
    },
    {
      "page": "graphNicheLR.dgCMatrix",
      "title": "Sub function for graphNicheLR, input a sparse matrix",
      "topics": [
        "graphNicheLR.dgCMatrix"
      ]
    },
    {
      "page": "heatmap_GO",
      "title": "Show significant genes across top GO term hits with coefficients from regression analysis of an interaction",
      "topics": [
        "heatmap_GO"
      ]
    },
    {
      "page": "hex_bin",
      "title": "GGPLOT2 FUNCTIONALITY FOR MAPPING TO HEXAGON SIZE AND COLOUR AESTHETICS by Robin Edwards, 2013 (geotheory.co.uk, @geotheory) This has been adapted from the ggplot bin_hex.R script that underpins geom_hex, etc (see https://github.com/hadley/densityvis/blob/master/R/bin-hex.r).",
      "topics": [
        "hex_bin"
      ]
    },
    {
      "page": "ImpData-class",
      "title": "The ImpData Class",
      "topics": [
        "ImpData",
        "ImpData-class"
      ]
    },
    {
      "page": "imputeLR",
      "title": "Impute the L or R value from the nearest neighbors of each location",
      "topics": [
        "imputeLR"
      ]
    },
    {
      "page": "imputeNiche",
      "title": "Impute the data",
      "topics": [
        "imputeNiche"
      ]
    },
    {
      "page": "imputeNicheVelo",
      "title": "Impute the velocity mtx using the specified method",
      "topics": [
        "imputeNicheVelo"
      ]
    },
    {
      "page": "imputeNicheVelo.CytoSignal",
      "title": "Sub function for imputeNicheVelo, input a Cytosignal object",
      "topics": [
        "imputeNicheVelo.CytoSignal"
      ]
    },
    {
      "page": "imputeVeloLR",
      "title": "Impute time derivative of L or R from the nearest neighbors of each location",
      "topics": [
        "imputeVeloLR"
      ]
    },
    {
      "page": "inferCorrScore",
      "title": "Infer the correspondence between LR-scores and Significance",
      "topics": [
        "inferCorrScore"
      ]
    },
    {
      "page": "inferEpsParams",
      "title": "Infer the parameters of the Gaussian kernel",
      "topics": [
        "inferEpsParams"
      ]
    },
    {
      "page": "inferIntrDEG",
      "title": "Infer significant genes (or TFs) for each interaction",
      "topics": [
        "inferIntrDEG"
      ]
    },
    {
      "page": "inferIntrScore",
      "title": "Calculate LRScore from the imputed L and R values",
      "topics": [
        "inferIntrScore"
      ]
    },
    {
      "page": "inferIntrVelo",
      "title": "Calculate the interaction velocity from the imputed time derivative of L or R values",
      "topics": [
        "inferIntrVelo"
      ]
    },
    {
      "page": "inferNullScoreLR",
      "title": "Permute LR score for specific ligand-receptor imputation obj pairs",
      "topics": [
        "inferNullScoreLR"
      ]
    },
    {
      "page": "inferScoreLR",
      "title": "Compute the LR score for specific ligand-receptor imputation pairs",
      "topics": [
        "inferScoreLR"
      ]
    },
    {
      "page": "inferSignif",
      "title": "Infer significance of LR scores",
      "topics": [
        "inferSignif"
      ]
    },
    {
      "page": "inferSpatialCorr",
      "title": "Infer the correspondence between LR-scores and Significance",
      "topics": [
        "inferSpatialCorr"
      ]
    },
    {
      "page": "inferVeloLR",
      "title": "Sub function for inferVeloLR, input a CytoSignal object",
      "topics": [
        "inferVeloLR"
      ]
    },
    {
      "page": "lrScores-class",
      "title": "The lrScores Class",
      "topics": [
        "lrScores",
        "lrScores-class"
      ]
    },
    {
      "page": "lrVelo-class",
      "title": "The lrvelo Class",
      "topics": [
        "lrVelo",
        "lrVelo-class"
      ]
    },
    {
      "page": "mergeCytoSignal",
      "title": "Merge multiple CytoSignal objects for cross-dataset analysis",
      "topics": [
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    },
    {
      "page": "mergedCytoSignal-class",
      "title": "mergedCytoSignal Class for cross-dataset analysis of spatial cell-cell communication",
      "topics": [
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      "page": "names.mergedCytoSignal",
      "title": "Dataset names of a mergedCytoSignal object",
      "topics": [
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        "names<-.mergedCytoSignal"
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      "page": "permuteLR",
      "title": "Permute Imputation Results of specific imputation method",
      "topics": [
        "permuteLR"
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    },
    {
      "page": "plotCircosNIntr",
      "title": "Make Circos plot summarising number of interactions between clusters",
      "topics": [
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