Package index • CellSPA

All functions
`CellSPA()`	A wrapper function to calculate all metrics
`calAggExpressionCorrelation()`	Calculate association with the reference for the aggregated profile
`calBaselineAllMetrics()`	Calculate the baseline metrics of cell from cell segmentation output
`calBaselineCellMetrics()`	Calculate the baseline metrics of segmented cell from cell segmentation output
`calBaselineCellShapeMetrics()`	Calculate the baseline metrics of cell shapes from cell segmentation output
`calExpressionCorrelation()`	Calculate association with the reference
`calMarkerPct()`	Calculate marker expression purity for each cell given a marker list
`calMarkerPurity()`	Calculate marker purity for each cell given a marker list
`calNegMarkerVsDist()`	Calculate the spatial diversity of base line metrics
`calSpatialMetricsDiversity()`	Calculate the spatial diversity of base line metrics
`generateMarkerList()`	Generating marker list using the reference data
`generatePolygon()`	Generating polygon
`processingRef()`	Preprocessing the the reference scRNA-seq data
`processingSPE()`	Preprocessing the the spatial experiment data.
`readBIDCell()`	Read BIDCell output
`readMatrixMask_per_sample()`	Preprocessing the the spatial experiment data for cell-level expression matrix with mask output.
`readSimpleSeg()`	Preprocessing the the spatial experiment data for SimpleSeg output.
`readSimpleSeg_per_sample()`	Preprocessing the the spatial experiment data for SimpleSeg output (per sample).
`readTiffOutput()`	Read Tiff output from BIDCell
`readVizgen()`	Read Vizgen output
`readXenium()`	Read Xenium output
`spe`	An example SpatialExperiment data
`subset()`	Subset Spatial experiment object by column

Reference

All functions