Spatially-aware normalisation for spatial transcriptomics data

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Documentation for package ‘SpaNorm’ version 1.7.4

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

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