Package index
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HumanDLPFC - Human dorsolateral prefrontal cortex (DLPFC) visium sample
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SpaNorm() - Spatially-dependent normalisation for spatial transcriptomics data
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`$`(<SpaNormFit>) - An S4 class to store a SpaNorm model fit
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SpaNormPCA() - GLM-based (SpaNorm) PCA
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SpaNormSVG() - Model-based spatially variable gene (SVG) calling
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calculateMu() - Compute fitted means from a negative binomial GLM fit
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fastSizeFactors() - Filter genes based on expression
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filterGenes() - Filter genes based on expression
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fitNB() - Fit a per-gene negative binomial GLM
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invert_mat() - Invert a symmetric positive-definite matrix
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plotCovariate() - Diagnostic plot of predicted expression for a covariate
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plotSpatial() - Plot spatial transcriptomic annotations per spot
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topSVGs() - Export top SVG results to a data frame