Package: path2path 0.99.4

path2path: Directional Pathway-by-Pathway Interaction Maps from Genome-Scale Perturb-Seq

Builds a directional pathway-by-pathway interaction map from genome-scale Perturb-seq differential-expression statistics by two stacked runs of preranked gene set enrichment analysis: once per perturbation over genes, then once per readout pathway over perturbations. Entry (j,k) of the resulting matrix measures whether perturbations targeting pathway j's members produce a coordinated transcriptional response in pathway k. The package includes target exclusion, effective-size filters, overlap masking, Stage 2 p-values with false-discovery-rate control, and a whole-pipeline permutation calibration with generalized-Pareto tail estimation.

Authors:Jun Li [aut, cre]