Package: path2path
Type: Package
Title: Directional Pathway-by-Pathway Interaction Maps from
        Genome-Scale Perturb-Seq
Version: 0.99.4
Authors@R: person("Jun", "Li", email = "jun.li@nd.edu",
    role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4353-5761"))
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.4.0)
Imports: fgsea, msigdbr, data.table, BiocParallel, withr, methods,
        stats, utils, grDevices, graphics
Suggests: ggplot2, testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle,
        SummarizedExperiment, R.utils
VignetteBuilder: knitr
biocViews: Software, GeneSetEnrichment, Pathways, CRISPR, SingleCell,
        DifferentialExpression, Transcriptomics, NetworkInference,
        GeneExpression, GeneTarget, KEGG, WholeGenome
URL: https://github.com/jli-stat/path2path
BugReports: https://github.com/jli-stat/path2path/issues
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
NeedsCompilation: no
Author: Jun Li [aut, cre] (<https://orcid.org/0000-0003-4353-5761>)
Maintainer: Jun Li <jun.li@nd.edu>
git_url: https://git.bioconductor.org/packages/path2path
git_branch: devel
git_last_commit: 7d979ae
git_last_commit_date: 2026-10-09
Repository: Bioconductor 3.24
Date/Publication: 2026-10-21
Packaged: 2026-10-21 23:33:19 UTC; biocbuild
