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