R reference

Normalisation

HumanDLPFC	Human dorsolateral prefrontal cortex (DLPFC) visium sample
SpaNorm	Spatially-dependent normalisation for spatial transcriptomics data
SpaNormFit	An S4 class to store a SpaNorm model fit

SVGs and PCA

getSVGResults	Get SVG results from a SpatialExperiment object
SpaNormPCA	GLM-based (SpaNorm) PCA
SpaNormSVG	Model-based spatially variable gene (SVG) calling
topSVGs	Export top SVG results to a data frame

Polishing

isPolished	Does a SpaNormFit carry a converged per-gene polish?
nbBlockDesign	A design with a per-group block, in compact form
nbMuFloor	The floor on a fitted negative binomial mean
nbNewtonSolver	Penalised NB Newton solvers and batched grams (for package developers)
nbProfilePsi	Profile-ML dispersion at fixed coefficients, blocked over genes
polishNB	Converge every gene of a shared negative binomial fit to its own optimum
polishSpaNorm	Converge each gene of a SpaNorm fit to its own optimum

Model fitting and helpers

calculateMu	Compute fitted means from a negative binomial GLM fit
fastSizeFactors	Filter genes based on expression
filterGenes	Filter genes based on expression
fitNB	Fit a per-gene negative binomial GLM
nbDevianceMoments	First two moments of the NB unit deviance, by direct summation
nbUnitDeviance	NB unit deviance
qlDispersion	Per-gene quasi-likelihood dispersion
qlMomentTable	A shared table of NB deviance moments
tpsBasis	Thin-plate-style tensor spline basis over spatial coordinates

Plotting

plotCovariate	Diagnostic plot of predicted expression for a covariate
plotSpatial	Plot spatial transcriptomic annotations per spot

GPU and backend

add_vec_mat_gpu	Broadcast-add a vector to a matrix, GPU-aware
checkGPU	Is an accelerated (GPU) torch device in use?
diag_mat	Build a diagonal matrix from a vector, GPU-aware
dnbinom_gpu	Negative binomial density (mean/size parameterisation), GPU-aware
getBackendDevice	Resolve the active torch backend device
getBackendDtype	Resolve the active torch backend dtype
getGPUMemoryBudget	Determine the accelerator memory budget for blocked fitting
gpuDtypeBytes	Bytes per element for the active backend dtype
hasBadValues	Does an object hold any NA/NaN/Inf?
invert_mat	Invert a symmetric positive-definite matrix
invert_mat_batched	Invert a batch of symmetric positive-definite matrices
is_torch_tensor	Is an object a torch tensor?
matmul_gpu	Tensor-aware matrix multiplication
mult_vec_mat_gpu	Broadcast-multiply a vector and a matrix, GPU-aware
resetGPUCache	Clear the cached GPU device/memory-budget state
rowSums_gpu	Row sums, GPU-aware
setGPUMemoryBudget	Set the accelerator memory budget for blocked fitting
tcrossprod_gpu	Tensor-aware tcrossprod
toGPUMatrix	Convert a matrix to a torch tensor on the active backend
toGPUVector	Convert a vector to a torch tensor on the active backend
toRMatrix	Convert a torch tensor (or R object) to a base R matrix