Package: pathfindR
Type: Package
Title: Enrichment Analysis Utilizing Active Subnetworks
Version: 3.0.2.9000
Authors@R: c(person("Ege", "Ulgen",
                    role = c("cre", "cph"), 
                    email = "egeulgen@gmail.com",
                    comment = c(ORCID = "0000-0003-2090-3621")),
             person("Ozan", "Ozisik",
                    role = "aut",
                    email = "ozanytu@gmail.com",
                    comment = c(ORCID = "0000-0001-5980-8002")))
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Description: Enrichment analysis enables researchers to uncover
        mechanisms underlying a phenotype. However, conventional
        methods for enrichment analysis do not take into account
        protein-protein interaction information, resulting in
        incomplete conclusions. 'pathfindR' is a tool for enrichment
        analysis utilizing active subnetworks. The main function
        identifies active subnetworks in a protein-protein interaction
        network using a user-provided list of genes and associated p
        values. It then performs enrichment analyses on the identified
        subnetworks, identifying enriched terms (i.e. pathways or, more
        broadly, gene sets) that possibly underlie the phenotype of
        interest. 'pathfindR' also offers functionalities to cluster
        the enriched terms and identify representative terms in each
        cluster, to score the enriched terms per sample and to
        visualize analysis results. The enrichment, clustering and
        other methods implemented in 'pathfindR' are described in
        detail in Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR': An
        R Package for Comprehensive Identification of Enriched Pathways
        in Omics Data Through Active Subnetworks. Front. Genet.
        <doi:10.3389/fgene.2019.00858>.
License: MIT + file LICENSE
URL: https://egeulgen.github.io/pathfindR/,
        https://github.com/egeulgen/pathfindR
BugReports: https://github.com/egeulgen/pathfindR/issues
Encoding: UTF-8
LazyData: true
biocViews:
Imports: DBI, AnnotationDbi, doParallel, foreach, rmarkdown, ggplot2,
        ggraph, ggupset, ggnewscale, fpc, ggkegg (>= 1.4.0), grDevices,
        httr, igraph, R.utils, msigdbr (>= 24.1.0), knitr, Rcpp
Depends: R (>= 4.3.0), pathfindR.data (>= 2.2.0)
Suggests: org.Hs.eg.db, testthat (>= 3.0.0), covr, mockery
VignetteBuilder: knitr
LinkingTo: Rcpp
Config/testthat/parallel: true
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libmagick++-dev gsfonts
        libicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        zlib1g-dev
Repository: https://egeulgen.r-universe.dev
Date/Publication: 2026-07-02 06:44:08 UTC
RemoteUrl: https://github.com/egeulgen/pathfindr
RemoteRef: HEAD
RemoteSha: 9bcdd9180ecfae32d472f738cfe2fd3476d64e26
NeedsCompilation: yes
Packaged: 2026-07-02 10:08:21 UTC; root
Author: Ege Ulgen [cre, cph] (ORCID: <https://orcid.org/0000-0003-2090-3621>),
  Ozan Ozisik [aut] (ORCID: <https://orcid.org/0000-0001-5980-8002>)