Background
We developed InSituCor as a tool for exploratory analysis of CosMx data; it has since become a mainstay of our in-house analyses. InSituCor reports on modules of “spatially correlated” genes, i.e. genes that tend to be expressed in the same tissue regions as each other. We have found it to be a consistently useful tool for discovering unexpected relationships in CosMx data.
InSituCor makes one important contribution to the spatial correlation field: it isolates correlations that can’t be explained by the cell type landscape alone. While the results of legacy methods are dominated by uninteresting results (e.g., “all the plasma cell markers are spatially correlated with each other”), InSituCor ignores these trivial findings, returning a more concise, and much more interesting manifest of spatial correlations.
InSituCor is available as both an R package and a custom module for AtoMx.