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The semi-parametric\nkernel machine regression model is a powerful tool for\ncapturing these types of relationships. They provide a\nframework for testing for relationships between outcomes of\ninterest and high dimensional data such as metabolomic,\ngenomic, or proteomic pathways. PaIRKAT uses known biological\nconnections between high dimensional variables by representing\nthem as edges of ‘graphs’ or ‘networks.’ It is common for nodes\n(e.g. metabolites) to be disconnected from all others within\nthe graph, which leads to meaningful decreases in testing power\nwhether or not the graph information is included. We include a\ngraph regularization or ‘smoothing’ approach for managing this\nissue.", "License": "GPL-3", "Encoding": "UTF-8", "BugReports": "https://github.com/Ghoshlab/pairkat/issues", "biocViews": "Software, Metabolomics, KEGG, Pathways, Network,\nGraphAndNetwork, Regression", "RoxygenNote": "7.1.2", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libglpk-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:57:08 UTC", "RemoteUrl": "https://github.com/bioc/pairkat", "RemoteRef": "HEAD", "RemoteSha": "56ad567b6ad3ec29039967dcdc451737f3c78642", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:13:44 UTC", "User": "root" }, "Author": "Charlie Carpenter [aut],\nCameron Severn [aut],\nMax McGrath [cre, aut]", "Maintainer": "Max McGrath ", "MD5sum": "6555b856039becebdd61b3406f411b25", "_user": "bioc", "_type": "src", "_file": "pairkat_1.19.0.tar.gz", "_fileid": "adec54f2955167d9705691cbc50e261de2e01345bf647ab7544cf547e80002ff", "_filesize": 708770, "_sha256": "adec54f2955167d9705691cbc50e261de2e01345bf647ab7544cf547e80002ff", "_created": "2026-05-30T07:13:44.000Z", "_published": "2026-05-30T10:47:52.279Z", "_jobs": [ { "job": 78632757014, "time": 168, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7306392357" }, { "job": 78632757025, "time": 872, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7306471854" }, { "job": 78632757020, "time": 831, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7306466735" }, { "job": 78632757030, "time": 661, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7307433287" }, { "job": 78632757026, "time": 664, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7307433753" }, { "job": 78632378613, "time": 416, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306371998" }, { "job": 78632757009, "time": 125, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306387505" }, { "job": 78632757021, "time": 1075, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7306494017" }, { "job": 78632757027, "time": 1064, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7306492804" }, { "job": 78632757034, "time": 860, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7306470515" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677654827", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/pairkat", "_commit": { "id": "56ad567b6ad3ec29039967dcdc451737f3c78642", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381028 }, "_maintainer": { "name": "Max McGrath", "email": "max.mcgrath@ucdenver.edu" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "KEGGREST", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "CompQuadForm", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.19.0", "bioc": "3.24" }, { "branch": "release", "version": "1.18.0", "bioc": "3.23" } ], "_topics": [ "software", "metabolomics", "kegg", "pathways", "network", "graphandnetwork", "regression" ], "_stars": 0, "_contributors": [ { "user": "cameronsevern", "count": 15, "uuid": 27509674 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 319, "source": "https://www.bioconductor.org/packages/stats/bioc/pairkat" }, "_devurl": "https://github.com/ghoshlab/pairkat", "_searchresults": 1, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/pairkat.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "GatherNetworks", "PaIRKAT", "plotNetworks" ], "_datasets": [ { "name": "smokers", "title": "Smokers - 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