# Spatially-aware normalisation for spatial transcriptomics data

## 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