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  "Title": "Directional Pathway-by-Pathway Interaction Maps from\nGenome-Scale Perturb-Seq",
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  "Authors@R": "person(\"Jun\", \"Li\", email = \"jun.li@nd.edu\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4353-5761\"))",
  "Description": "Builds a directional pathway-by-pathway interaction map\nfrom genome-scale Perturb-seq differential-expression\nstatistics by two stacked runs of preranked gene set enrichment\nanalysis: once per perturbation over genes, then once per\nreadout pathway over perturbations. Entry (j,k) of the\nresulting matrix measures whether perturbations targeting\npathway j's members produce a coordinated transcriptional\nresponse in pathway k. The package includes target exclusion,\neffective-size filters, overlap masking, Stage 2 p-values with\nfalse-discovery-rate control, and a whole-pipeline permutation\ncalibration with generalized-Pareto tail estimation.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, GeneSetEnrichment, Pathways, CRISPR, SingleCell,\nDifferentialExpression, Transcriptomics, NetworkInference,\nGeneExpression, GeneTarget, KEGG, WholeGenome",
  "URL": "https://github.com/jli-stat/path2path",
  "BugReports": "https://github.com/jli-stat/path2path/issues",
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  "Author": "Jun Li [aut, cre] (<https://orcid.org/0000-0003-4353-5761>)",
  "Maintainer": "Jun Li <jun.li@nd.edu>",
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  "Date/Publication": "2026-10-10 02:03:24 UTC",
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      ]
    },
    {
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      ]
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      "topics": [
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    },
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      "title": "Whole-pipeline permutation null calibration.",
      "topics": [
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      "topics": [
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    {
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      "topics": [
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      ]
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      "topics": [
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    {
      "page": "order_by_activity",
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      "topics": [
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