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>
Config/pak/sysreqs: libssl-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-10 02:03:24 UTC
RemoteUrl: https://github.com/BiocStaging/path2path
RemoteRef: HEAD
RemoteSha: 7d979ae4573a0ee936aaf9dfb40fa672f388435e
Packaged: 2026-10-10 07:28:23 UTC; root