Package index

Main analysis

Run the BLISA cell-cell communication workflow.

blisa()

Run BLISA spatial cell-cell communication analysis

Preprocessing

Binning, spatial weights, and ligand-receptor pair filtering.

hexBinCells()

Bin cells into hexagonal spatial bins

visiumSpotBins()

Build spot-level hexagonal bins from a Visium SpatialExperiment

computeSpatialWeights()

Compute Spatial Weights for BLISA

filterLRpairs()

Filter ligand-receptor pairs by expression threshold

Cell-cell interaction scoring

runCCI()

Score cell-cell interactions from BLISA hotspots

Pathway-level analysis

Aggregate BLISA hotspots to the pathway level.

blisaPathway()

Aggregate BLISA hotspots to the pathway level

Visualisation

Spatial maps and heatmaps of hotspots and interactions.

plotHotspots()

Spatial hotspot map for one ligand-receptor pair

plotLRrank()

Dot plot ranking LR pairs by number of significant hotspot bins

plotCCI()

Heatmap of CCI scores across all ligand-receptor pairs

plotCCILR()

Sender-by-receiver heatmap of CCI scores for one ligand-receptor pair

plotCCIsummary()

Sender-by-receiver heatmap of aggregated CCI scores across LR pairs

plotCCIspatial()

Spatial map of dominant sender-receiver cell-type pairs at BLISA hotspots

Utilities

is.blisa()

Test if an object is a blisa object

blisa-package

blisa: Bivariate Local Indicator of Spatial Association for spatial transcriptomics