Package index
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show(<PACEFit>) - PACEFit: a fitted PACE model
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ambientField() - Build the ambient contamination field
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anchorGenes() - Contamination anchor genes per cell type
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buildNeighbourhood() - Build the neighbourhood kernels
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cellContamination() - Per-cell contamination
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neighbourSlopes() - Shrunken neighbour proximity slopes
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paceDecompose() - Variance decomposition
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paceDrivers() - Per-pair driver scores
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paceFit() - Fit a PACE model to a SpatialExperiment
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paceModel() - Fit the PACE model
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paceModelGaussian() - Fit the PACE model to continuous intensities
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paceShrink() - Shrink the neighbour slopes
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pairVariance() - Pairwise spatial variance table
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plotDecomposition() - Per-focal variance decomposition plot
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plotDrivers() - Per-pair driver composite
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plotPairHeatmap() - Pairwise spatial-percent heatmap
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plotProximity() - Expression versus number of neighbours (per-bin boxplot)
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plotResponseCurve() - Response curve: binned means with the PACE slope overlaid
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plotResponseMap() - Tissue maps and scatters for one exemplar image per arm
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topDrivers() - Per-pair driver tables
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varianceDecomposition() - Per-gene variance decomposition