Proximity-Associated Changes in Expression for Spatial Transcriptomics

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Documentation for package ‘PACE’ version 0.99.20

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

Help Pages

ambientField	Build the ambient contamination field
ambientField-method	Build the ambient contamination field
anchorGenes	Contamination anchor genes per cell type
buildNeighbourhood	Build the neighbourhood kernels
buildNeighbourhood-method	Build the neighbourhood kernels
cellContamination	Per-cell contamination
cellContamination-method	Per-cell contamination
cellTypes	Cell types modelled
cellTypes-method	Cell types modelled
compactFit	Drop the per-cell matrices from a fit
fitState	Raw solver state
fitState-method	Raw solver state
neighbourSlopes	Shrunken neighbour proximity slopes
neighbourSlopes-method	Shrunken neighbour proximity slopes
neighbourSlopes<-	Shrunken neighbour proximity slopes
neighbourSlopes<--method	Shrunken neighbour proximity slopes
paceDecompose	Variance decomposition
paceDecompose-method	Variance decomposition
paceDrivers	Per-pair driver scores
paceDrivers-method	Per-pair driver scores
PACEFit	PACEFit: a fitted PACE model
paceFit	Fit a PACE model to a SpatialExperiment
PACEFit-class	PACEFit: a fitted PACE model
paceFit-method	Fit a PACE model to a SpatialExperiment
paceModel	Fit the PACE model
paceModel-method	Fit the PACE model
paceModelGaussian	Fit the PACE model to continuous intensities
paceModelGaussian-method	Fit the PACE model to continuous intensities
paceParams	Fitting parameters
paceParams-method	Fitting parameters
paceShrink	Shrink the neighbour slopes
paceShrink-method	Shrink the neighbour slopes
pairVariance	Pairwise spatial variance table
pairVariance-method	Pairwise spatial variance table
plotDecomposition	Per-focal variance decomposition plot
plotDrivers	Per-pair driver composite
plotPairHeatmap	Pairwise spatial-percent heatmap
plotProximity	Expression versus number of neighbours (per-bin boxplot)
plotResponseCurve	Response curve: binned means with the PACE slope overlaid
plotResponseMap	Tissue maps and scatters for one exemplar image per arm
show-method	PACEFit: a fitted PACE model
stashPACE	Stash PACE readouts in a SpatialExperiment
topDrivers	Per-pair driver tables
topDrivers-method	Per-pair driver tables
topDrivers<-	Per-pair driver tables
topDrivers<--method	Per-pair driver tables
varianceDecomposition	Per-gene variance decomposition
varianceDecomposition-method	Per-gene variance decomposition
varianceDecomposition<-	Per-gene variance decomposition
varianceDecomposition<--method	Per-gene variance decomposition