{ "_id": "6a1eedc0b401979e73412847", "Package": "PathwayVote", "Title": "Robust Pathway Enrichment for DNA Methylation Studies Using\nEnsemble Voting", "Version": "0.1.3", "Authors@R": "c(person(\"Yinan\", \"Zheng\",\nemail = \"y-zheng@northwestern.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-2006-7320\")))", "Description": "Performs pathway enrichment analysis using a voting-based\nframework that integrates CpG–gene regulatory information from\nexpression quantitative trait methylation (eQTM) data. For a\ngrid of top-ranked CpGs and filtering thresholds, gene sets are\ngenerated and refined using an entropy-based pruning strategy\nthat balances information richness, stability, and probe bias\ncorrection. In particular, gene lists dominated by genes with\ndisproportionately high numbers of CpG mappings are penalized\nto mitigate active probe bias—a common artifact in methylation\ndata analysis. Enrichment results across parameter combinations\nare then aggregated using a voting scheme, prioritizing\npathways that are consistently recovered under diverse settings\nand robust to parameter perturbations.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://yinanzheng.r-universe.dev", "Date/Publication": "2026-01-19 16:33:30 UTC", "RemoteUrl": "https://github.com/yinanzheng/pathwayvote", "RemoteRef": "HEAD", "RemoteSha": "4b84a436e33e8a72104d7b7a2f41525b470609bc", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-19 09:08:33 UTC", "User": "root" }, "Author": "Yinan Zheng [aut, cre] (ORCID: )", "Maintainer": "Yinan Zheng ", "MD5sum": "c341de356c74815961dd52a43576dd1d", "_user": "yinanzheng", "_type": "src", "_file": "PathwayVote_0.1.3.tar.gz", "_fileid": "6485f391032ae69f55ffd71e68be82e4719f6cc8170bfb9727145d242a3b8856", "_filesize": 115590, "_sha256": "6485f391032ae69f55ffd71e68be82e4719f6cc8170bfb9727145d242a3b8856", "_created": "2026-05-19T09:08:33.000Z", "_published": "2026-06-02T14:50:40.899Z", "_distro": "noble", "_jobs": [ { "job": 79099054213, "time": 316, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7079433942" }, { "job": 79099053929, "time": 317, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7079433993" }, { "job": 79099055145, "time": 224, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7079391990" }, { "job": 79099053936, "time": 356, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7079431304" }, { "job": 79099053437, "time": 304, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7079320086" }, { "job": 79099053404, "time": 253, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7361196907" }, { "job": 79099054070, "time": 249, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7079409283" }, { "job": 79099054735, "time": 294, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7079425532" }, { "job": 79099053878, "time": 242, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7079407342" } ], "_buildurl": "https://github.com/r-universe/yinanzheng/actions/runs/26087326649", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/yinanzheng/pathwayvote", "_commit": { "id": "4b84a436e33e8a72104d7b7a2f41525b470609bc", "author": "Yinan Zheng ", "committer": "Yinan Zheng ", "message": "Add Excel export for pathway_vote results\n\nIntroduced the write_enrich_results_xlsx() function to export pathway_vote results to a multi-sheet Excel file using openxlsx. Updated pathway_vote to include a CpG-Gene mapping table with enrichment annotations, improved documentation, and removed in-function readable mapping from run_enrichment in favor of post-processing.\n", "time": 1768840410 }, "_maintainer": { "name": "Yinan Zheng", "email": "y-zheng@northwestern.edu", "login": "yinanzheng", "description": "AbbVie ｜ Northwestern University", "uuid": 7666261, "orcid": "0000-0002-2006-7320" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "harmonicmeanp", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "clusterProfiler", "role": "Imports" }, { "package": "future", "role": "Imports" }, { "package": "furrr", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "parallelly", "role": "Imports" }, { "package": "GO.db", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "reactome.db", "role": "Suggests" }, { "package": "openxlsx", "role": "Suggests" } ], "_owner": "yinanzheng", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-26", "n": 6 }, { "week": "2025-36", "n": 1 }, { "week": "2025-37", "n": 6 }, { "week": "2026-03", "n": 2 }, { "week": "2026-04", "n": 1 } ], "_tags": [ { "name": "v0.1.2", "date": "2025-09-13" } ], "_stars": 0, "_contributors": [ { "user": "yinanzheng", "count": 71, "uuid": 7666261 } ], "_userbio": { "uuid": 7666261, "type": "user", "name": "Yinan Zheng", "description": "AbbVie ｜ Northwestern University" }, "_downloads": { "count": 156, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PathwayVote" }, "_devurl": "https://github.com/yinanzheng/pathwayvote", "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/PathwayVote.html", "manual.pdf" ], "_homeurl": "https://github.com/yinanzheng/pathwayvote", 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