Package: PACE 0.99.20

PACE: Proximity-Associated Changes in Expression for Spatial Transcriptomics

PACE (Proximity-Associated Changes in Expression) is a hierarchical empirical Bayes framework that quantifies how a cell's gene expression changes with proximity to specific neighbouring cell types in imaging-based spatial transcriptomics such as Xenium and CosMx. It fits negative binomial mixed models with partial pooling across cell types, corrects for transcript contamination between adjacent cells with a per-cell ambient term, and decomposes expression variance into cell-type identity, spatial cell state, contamination, and residual components. Input and output follow SpatialExperiment conventions.

Authors:Elijah Willie [aut, cre], Shreya Rajesh Rao [aut], John Ormerod [aut], Ellis Patrick [aut], Australian Government Research Training Program [fnd]