{ "_id": "6a15493facfb0bcc41d584c4", "Package": "IHW", "Title": "Independent Hypothesis Weighting", "Version": "1.29.0", "Authors@R": "c(person(\"Nikos\", \"Ignatiadis\", email = \"nikos.ignatiadis01@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Wolfgang\", \"Huber\", role = \"aut\"))", "Description": "Independent hypothesis weighting (IHW) is a multiple\ntesting procedure that increases power compared to the method\nof Benjamini and Hochberg by assigning data-driven weights to\neach hypothesis. The input to IHW is a two-column table of\np-values and covariates. The covariate can be any\ncontinuous-valued or categorical variable that is thought to be\ninformative on the statistical properties of each hypothesis\ntest, while it is independent of the p-value under the null\nhypothesis.", "License": "Artistic-2.0", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncology, MultipleComparison, RNASeq", "RoxygenNote": "7.1.1", "Config/pak/sysreqs": "coinor-symphony coinor-libsymphony-dev", "Repository": "https://huber-group-embl.r-universe.dev", "Date/Publication": "2023-04-25 14:43:54 UTC", "RemoteUrl": "https://github.com/nignatiadis/IHW", "RemoteRef": "HEAD", "RemoteSha": "2da27aa7d23c399be0e5f8ae33aa1b61aeacc389", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-26 07:12:50 UTC", "User": "root" }, "Author": "Nikos Ignatiadis [aut, cre],\nWolfgang Huber [aut]", "Maintainer": "Nikos Ignatiadis ", "MD5sum": "65babdd0af22aae87c247d6495aaee3d", "_user": "huber-group-embl", "_type": "src", "_file": "IHW_1.29.0.tar.gz", "_fileid": "76826cccf43ebd8db44f24d860edb2ea785e66bd17b2bebe6216f0ab1f476602", "_filesize": 3906129, "_sha256": "76826cccf43ebd8db44f24d860edb2ea785e66bd17b2bebe6216f0ab1f476602", "_created": "2026-05-26T07:12:50.000Z", "_published": "2026-05-26T07:18:23.521Z", "_distro": "noble", "_jobs": [ { "job": 77825090129, "time": 203, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7211020945" }, { "job": 77825090160, "time": 208, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7211022675" }, { "job": 77825090152, "time": 143, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7211002783" }, { "job": 77825090068, "time": 124, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7210996836" }, { "job": 77824478095, "time": 273, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7210962973" }, { "job": 77825090055, "time": 156, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7211006750" }, { "job": 77825090130, "time": 297, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7211047075" }, { "job": 77825090131, "time": 299, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7211047372" }, { "job": 77825090179, "time": 163, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7211009071" } ], "_buildurl": "https://github.com/r-universe/huber-group-embl/actions/runs/26437757026", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/nignatiadis/IHW", "_commit": { "id": "2da27aa7d23c399be0e5f8ae33aa1b61aeacc389", "author": "J Wokaty ", "committer": "J Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_17 branch\n", "time": 1682433834 }, "_maintainer": { "name": "Nikos Ignatiadis", "email": "nikos.ignatiadis01@gmail.com", "login": "nignatiadis", "description": "Statistician", "uuid": 2933625 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "slam", "role": "Imports" }, { "package": "lpsymphony", "role": "Imports" }, { "package": "fdrtool", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" }, { "package": "scales", "role": "Suggests" }, { "package": "DESeq2", "role": "Suggests" }, { "package": "airway", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "Matrix", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" } ], "_owner": "nignatiadis", "_selfowned": false, "_usedby": 2, "_updates": [], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.41.0", "bioc": "3.24" }, { "branch": "release", "version": "1.40.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "multiplecomparison", "rnaseq", "ihw", "pvalue-adjustment" ], "_stars": 16, "_contributors": [ { "user": "nignatiadis", "count": 18, "uuid": 2933625 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "dtenenba", "count": 4, "uuid": 2286826 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "kayla-morrell", "count": 1, "uuid": 32339524 }, { "user": "link-ny", "count": 1, "uuid": 4392950 } ], "_userbio": { "uuid": 57364287, "type": "organization", "name": "EMBL Huber Group", "description": "Repository for joint projects by members and ex-members of the Huber group at EMBL. Please see also individuals' pages for further repositories." }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/IHW" }, "_devurl": "https://github.com/nignatiadis/ihw", "_searchresults": 403, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/IHW.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "adj_pvalues", "alpha", "as.data.frame", "covariate_type", "covariates", "get_bh_threshold", "groups_by_filter", "groups_factor", "ihw", "m_groups", "nbins", "nfolds", "nrow", "plot", "pvalues", "regularization_term", "rejected_hypotheses", "rejections", "show", "thresholds", "weighted_pvalues", "weights" ], "_help": [ { "page": "get_bh_threshold", "title": "Data-driven threshold of Benjamini Hochberg Procedure", "topics": [ "get_bh_threshold" ] }, { "page": "groups_by_filter", "title": "Stratify hypotheses based on increasing value of the covariate", "topics": [ "groups_by_filter" ] }, { "page": "ihw.default", "title": "ihw: Main function for Independent Hypothesis Weighting", "topics": [ "ihw", "ihw.default", "ihw.formula" ] }, { "page": "ihw.DESeqResults", "title": "ihw.DESeqResults: IHW method dispatching on DESeqResults objects", "topics": [ "ihw.DESeqResults" ] }, { "page": "ihwResult-class", "title": "An S4 class to represent the ihw output.", "topics": [ "adj_pvalues", "adj_pvalues,ihwResult-method", "alpha", "alpha,ihwResult-method", "as.data.frame,ihwResult-method", "as.data.frame_ihwResult", "covariates", "covariates,ihwResult-method", "covariate_type", "covariate_type,ihwResult-method", "groups_factor", "groups_factor,ihwResult-method", "ihwResult", "ihwResult-class", "m_groups", "m_groups,ihwResult-method", "nbins", "nbins,ihwResult-method", "nfolds", "nfolds,ihwResult-method", "nrow,ihwResult-method", "pvalues", "pvalues,ihwResult-method", 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versus adjusted p-values", "FWER control with IHW", "Other data types, and how to choose the covariate", "Criteria for choosing a covariate", "Examples", "Why are the different covariate criteria necessary?", "Diagnostic plots for the covariate", "Scatter plots", "Stratified p-value histograms", "Further reading about appropriate covariates", "Advanced usage: Working with incomplete p-value lists", "References" ], "created": "2016-01-31 16:28:33", "modified": "2016-10-03 22:01:49", "commits": 15 } ], "_score": 8.131644323530955, "_indexed": false, "_nocasepkg": "ihw", "_universes": [ "huber-group-embl" ], "_indexurl": "https://bioc.r-universe.dev/IHW", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.29.0", "date": "2026-05-26T07:15:56.000Z", "distro": "noble", "commit": "2da27aa7d23c399be0e5f8ae33aa1b61aeacc389", "fileid": "5ca4d4d5b146a231e7cda623905dd294f4d28e70f017e5e226c3303e884941ed", "status": "success", "check": "NOTE", "buildurl": 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