Infer Cell-Cell Communication from Spatial Transcriptomics

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Documentation for package ‘blisa’ version 0.2.0

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blisa-package blisa: Bivariate Local Indicator of Spatial Association for spatial transcriptomics
blisa Run BLISA spatial cell-cell communication analysis
blisa.default Run BLISA spatial cell-cell communication analysis
blisa.SpatialExperiment Run BLISA spatial cell-cell communication analysis
computeSpatialWeights Compute Spatial Weights for BLISA
filterLRpairs Filter ligand-receptor pairs by expression threshold
hexBinCells Bin cells into hexagonal spatial bins
is.blisa Test if an object is a blisa object
plotCCI Heatmap of CCI scores across all ligand-receptor pairs
plotCCI.blisa Heatmap of CCI scores across all ligand-receptor pairs
plotCCI.default Heatmap of CCI scores across all ligand-receptor pairs
plotCCILR Sender-by-receiver heatmap of CCI scores for one ligand-receptor pair
plotCCILR.blisa Sender-by-receiver heatmap of CCI scores for one ligand-receptor pair
plotCCILR.default Sender-by-receiver heatmap of CCI scores for one ligand-receptor pair
plotCCIspatial Spatial map of dominant sender-receiver cell-type pairs at BLISA hotspots
plotCCIsummary Sender-by-receiver heatmap of aggregated CCI scores across LR pairs
plotCCIsummary.blisa Sender-by-receiver heatmap of aggregated CCI scores across LR pairs
plotCCIsummary.default Sender-by-receiver heatmap of aggregated CCI scores across LR pairs
plotHotspots Spatial hotspot map for one ligand-receptor pair
plotHotspots.blisa Spatial hotspot map for one ligand-receptor pair
plotLRrank Dot plot ranking LR pairs by number of significant hotspot bins
plotLRrank.blisa Dot plot ranking LR pairs by number of significant hotspot bins
plotLRrank.data.frame Dot plot ranking LR pairs by number of significant hotspot bins
runCCI Score cell-cell interactions from BLISA hotspots
runCCI.blisa Score cell-cell interactions from BLISA hotspots
runCCI.default Score cell-cell interactions from BLISA hotspots