Package index
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`$`(<SpiDEFit>) - An S4 class to store a single-bandwidth spiDE model fit
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`$`(<SpiDEResults>) - An S4 class to store multi-bandwidth spiDE results
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bandwidths() - Bandwidths used in a spiDE analysis
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buildNiches() - Build niche covariate matrices
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compositionTest() - Patient-level test of the between-sample composition association
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computeSizeFactors() - Compute per-sample library-size offsets
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fitSpiDE() - Fit the spiDE negative binomial model
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fits() - Extract per-bandwidth fits
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mergeNiches() - Merge niche cell-type columns into groups
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nicheDesign() - Build a spiDE design matrix
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polishSpiDE() - Converge an existing fit, gene by gene
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results() - Extract the tidy spiDE results table
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spiDE() - Run the full spiDE workflow
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spiGSEA() - Gene-set enrichment on a fitted spiDE model
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testSpiDE() - Test neighbourhood-dependent differential expression
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toySpiDE - A small synthetic SpatialExperiment for spiDE examples
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twoStageSpiDE() - Two-stage niche differential expression
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updateObject(<SpiDEFit>)updateObject(<SpiDEResults>) - Update a serialised spiDE object to the current class definition