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

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

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