Cross-Expression Analysis of Spatial Transcriptomics Data
Outputs a circular bullseye plot for a gene pair. The central circle i...
Calculates bullseye statistics for ALL gene pairs. Counts the number o...
Computes Pearson's correlation between pairs of columns. If one matrix...
Computes gene-gene correlations between cross-expressing cell-neighbor...
Computes cross-expression and co-expression p-values between all gene ...
Calculates the number of elements common between columns of two matric...
This function takes x and y coordinates and rotates them counterclockw...
Smooths cells' gene expression by averaging its expression by the near...
Determines whether the supplied genes show spatial enrichment in cross...
Plots gene expression and cross-expression on tissue by coloring cells...
Analyzes spatial transcriptomic data using cells-by-genes and cell location matrices to find gene pairs that coordinate their expression between spatially adjacent cells. It enables quantitative analysis and graphical assessment of these cross-expression patterns. See Sarwar et al. (2025) <doi:10.1101/2024.09.17.613579> and <https://github.com/gillislab/CrossExpression/> for more details.