{
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  "Package": "path2path",
  "Type": "Package",
  "Title": "Directional Pathway-by-Pathway Interaction Maps from\nGenome-Scale Perturb-Seq",
  "Version": "0.99.4",
  "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",
  "Config/testthat/edition": "3",
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  "NeedsCompilation": "no",
  "Author": "Jun Li [aut, cre] (<https://orcid.org/0000-0003-4353-5761>)",
  "Maintainer": "Jun Li <jun.li@nd.edu>",
  "Config/pak/sysreqs": "libssl-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-10 02:03:24 UTC",
  "RemoteUrl": "https://github.com/bioc/path2path",
  "RemoteRef": "HEAD",
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  "_published": "2026-10-21T21:30:14.719Z",
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    "email": "jun.li@nd.edu",
    "login": "jli-stat",
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    "uuid": 196732573,
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    "genesetenrichment",
    "pathways",
    "crispr",
    "singlecell",
    "differentialexpression",
    "transcriptomics",
    "networkinference",
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    "dataset_tag",
    "jaccard_mask",
    "load_pathways",
    "order_by_activity",
    "path2path",
    "pathway_jaccard",
    "permute_input",
    "plot_calibration",
    "plot_entry",
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    "read_input_matrix",
    "select_active",
    "stage1_nes",
    "stage2_matrix",
    "write_result"
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        "array"
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      "title": "Convert a SummarizedExperiment assay to a path2path input matrix.",
      "topics": [
        "as_path2path_matrix"
      ]
    },
    {
      "page": "as_path2path_se",
      "title": "Convert a path2path map to a SummarizedExperiment.",
      "topics": [
        "as_path2path_se"
      ]
    },
    {
      "page": "bh_populated",
      "title": "Benjamini-Hochberg over the populated (non-NA) cells of a matrix.",
      "topics": [
        "bh_populated"
      ]
    },
    {
      "page": "build_null_pool",
      "title": "Whole-pipeline permutation null calibration.",
      "topics": [
        "build_null_pool"
      ]
    },
    {
      "page": "calibrate_pvalues",
      "title": "One-call calibrated p-values for an existing map.",
      "topics": [
        "calibrate_pvalues"
      ]
    },
    {
      "page": "dataset_tag",
      "title": "Dataset tag from a zscore_<tag>.csv[.gz] filename.",
      "topics": [
        "dataset_tag"
      ]
    },
    {
      "page": "demo_pathways",
      "title": "Synthetic demonstration pathway collection",
      "topics": [
        "demo_pathways"
      ]
    },
    {
      "page": "demo_z",
      "title": "Synthetic demonstration input matrix",
      "topics": [
        "demo_z"
      ]
    },
    {
      "page": "jaccard_mask",
      "title": "Mask off-diagonal entries whose pathway pair overlaps above `tau`.",
      "topics": [
        "jaccard_mask"
      ]
    },
    {
      "page": "load_pathways",
      "title": "Load an MSigDB collection as a named list of gene-symbol vectors.",
      "topics": [
        "load_pathways"
      ]
    },
    {
      "page": "order_by_activity",
      "title": "Pathway names ordered by number of significant entries (descending).",
      "topics": [
        "order_by_activity"
      ]
    },
    {
      "page": "path2path",
      "title": "Full two-stage GSEA pipeline: z matrix -> pathway x pathway matrix.",
      "topics": [
        "path2path"
      ]
    },
    {
      "page": "pathway_jaccard",
      "title": "Pairwise Jaccard similarity of pathway gene sets (dense crossproduct).",
      "topics": [
        "pathway_jaccard"
      ]
    },
    {
      "page": "permute_input",
      "title": "Whole-matrix permutation: one global row and one global column permutation.",
      "topics": [
        "permute_input"
      ]
    },
    {
      "page": "plot_calibration",
      "title": "Route B diagnostics: null-pool tail versus the fitted GPD.",
      "topics": [
        "plot_calibration"
      ]
    },
    {
      "page": "plot_entry",
      "title": "GSEA-style enrichment plot for one map entry: why is M[j, k] strong?",
      "topics": [
        "plot_entry"
      ]
    },
    {
      "page": "plot_map",
      "title": "Heatmap of a path2path map with significance dots.",
      "topics": [
        "plot_map"
      ]
    },
    {
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      "topics": [
        "read_input_matrix"
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    },
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      "title": "Pathways with at least `min_sig` significant entries, as regulators and as readouts.",
      "topics": [
        "select_active"
      ]
    },
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      "title": "Stage 1: per-perturbation preranked GSEA.",
      "topics": [
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      "topics": [
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