{ "_id": "6a12abb5acfb0bcc41d17c41", "Package": "pathfindR", "Type": "Package", "Title": "Enrichment Analysis Utilizing Active Subnetworks", "Version": "2.7.0.9000", "Authors@R": "c(person(\"Ege\", \"Ulgen\",\nrole = c(\"cre\", \"cph\"),\nemail = \"egeulgen@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2090-3621\")),\nperson(\"Ozan\", \"Ozisik\",\nrole = \"aut\",\nemail = \"ozanytu@gmail.com\",\ncomment = c(ORCID = \"0000-0001-5980-8002\")))", "Maintainer": "Ege Ulgen ", "Description": "Enrichment analysis enables researchers to uncover\nmechanisms underlying a phenotype. However, conventional\nmethods for enrichment analysis do not take into account\nprotein-protein interaction information, resulting in\nincomplete conclusions. 'pathfindR' is a tool for enrichment\nanalysis utilizing active subnetworks. The main function\nidentifies active subnetworks in a protein-protein interaction\nnetwork using a user-provided list of genes and associated p\nvalues. It then performs enrichment analyses on the identified\nsubnetworks, identifying enriched terms (i.e. pathways or, more\nbroadly, gene sets) that possibly underlie the phenotype of\ninterest. 'pathfindR' also offers functionalities to cluster\nthe enriched terms and identify representative terms in each\ncluster, to score the enriched terms per sample and to\nvisualize analysis results. The enrichment, clustering and\nother methods implemented in 'pathfindR' are described in\ndetail in Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR': An\nR Package for Comprehensive Identification of Enriched Pathways\nin Omics Data Through Active Subnetworks. Front. Genet.\n.", "License": "MIT + file LICENSE", "URL": "https://egeulgen.github.io/pathfindR/,\nhttps://github.com/egeulgen/pathfindR", "BugReports": "https://github.com/egeulgen/pathfindR/issues", "Encoding": "UTF-8", "SystemRequirements": "Java (>= 8.0)", "biocViews": "", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libmagick++-dev gsfonts\ndefault-jdk libicu-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev zlib1g-dev", "Repository": "https://egeulgen.r-universe.dev", "Date/Publication": "2025-12-22 18:28:02 UTC", "RemoteUrl": "https://github.com/egeulgen/pathfindr", "RemoteRef": "HEAD", "RemoteSha": "7ce1330d6d168b01e1be174181c5fc6a8c027760", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-24 07:36:11 UTC", "User": "root" }, "Author": "Ege Ulgen [cre, cph] (ORCID: ),\nOzan Ozisik [aut] (ORCID: )", "MD5sum": "a0f6b8bfa3d15dffd80fe19c50add4d0", "_user": "egeulgen", "_type": 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