{ "_id": "6a195359acfb0bcc41de05ec", "Package": "kmcut", "Type": "Package", "Title": "Optimized Kaplan Meier analysis and identification and\nvalidation of prognostic biomarkers", "Version": "1.6.0", "Authors@R": "c(person(given = \"Igor\", family = \"Kuznetsov\", role = c(\"aut\", \"cre\"), email = \"ibkalb@gmail.com\"), person(given = \"Javed\", family = \"Khan\", role = \"aut\", email = \"khanjav@mail.nih.gov\"))", "Description": "The purpose of the package is to identify prognostic\nbiomarkers and an optimal numeric cutoff for each biomarker\nthat can be used to stratify a group of test subjects (samples)\ninto two sub-groups with significantly different survival\n(better vs. worse). The package was developed for the analysis\nof gene expression data, such as RNA-seq. However, it can be\nused with any quantitative variable that has a sufficiently\nlarge proportion of unique values.", "License": "Artistic-2.0", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "biocViews": "Software, StatisticalMethod, GeneExpression, Survival", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:03:31 UTC", "RemoteUrl": "https://github.com/bioc/kmcut", "RemoteRef": "RELEASE_3_23", "RemoteSha": "5bd54fd9c0d524247dee4994fc683b957694d1be", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:39:38 UTC", "User": "root" }, "Author": "Igor Kuznetsov [aut, cre],\nJaved Khan [aut]", "Maintainer": "Igor Kuznetsov ", "MD5sum": "15464bcc90b0979fba84a82eae24635a", "_user": "bioc-release", "_type": "src", "_file": "kmcut_1.6.0.tar.gz", "_fileid": "0679f10fc4cf43af9060d0333e453278ac551b65f1976f20d4b11db937226ce9", "_filesize": 1238139, "_sha256": "0679f10fc4cf43af9060d0333e453278ac551b65f1976f20d4b11db937226ce9", "_created": "2026-05-29T07:39:38.000Z", "_published": "2026-05-29T08:50:33.164Z", "_jobs": [ { "job": 78458828686, "time": 191, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7285655112" }, { "job": 78458828730, "time": 255, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7285673406" }, { "job": 78458828711, "time": 321, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7285691408" }, { "job": 78458828715, "time": 168, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7286800178" }, { "job": 78458828734, "time": 167, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7286810628" }, { "job": 78458326532, "time": 217, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285599008" }, { "job": 78458828660, "time": 107, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285631080" }, { "job": 78458828694, "time": 167, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7285648237" }, { "job": 78458828712, "time": 173, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7285650184" }, { "job": 78458828702, "time": 164, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7285647425" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624618415", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/kmcut", "_commit": { "id": "5bd54fd9c0d524247dee4994fc683b957694d1be", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381411 }, "_maintainer": { "name": "Igor Kuznetsov", "email": "ibkalb@gmail.com", "login": "ibkstore", "description": "", "uuid": 33561678 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "survival", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "pracma", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.7.0", "bioc": "3.24" }, { "branch": "release", "version": "1.6.0", "bioc": "3.23" } ], "_topics": [ "software", "statisticalmethod", "geneexpression", "survival" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 248, "source": "https://www.bioconductor.org/packages/stats/bioc/kmcut" }, "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/kmcut.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "create_se_object", "extract_columns", "extract_rows", "km_opt_pcut", "km_opt_scut", "km_qcut", "km_ucut", "km_val_cut", "transpose_table", "ucox_batch", "ucox_pred" ], "_help": [ { "page": "create_se_object", "title": "Create SummarizedExperiment object", "topics": [ "create_se_object" ] }, { "page": "extract_columns", "title": "Extract a sub-set of columns", "topics": [ "extract_columns" ] }, { "page": "extract_rows", "title": "Extract a sub-set of rows", "topics": [ "extract_rows" ] }, { "page": "km_opt_pcut", "title": "Find and evaluate optimal stratification cutoffs", "topics": [ "km_opt_pcut" ] }, { "page": "km_opt_scut", "title": "Find optimal stratification cutoffs", "topics": [ "km_opt_scut" ] }, { "page": "km_qcut", "title": "Apply quantile-based stratification cutoffs", "topics": [ "km_qcut" ] }, { "page": "km_ucut", "title": "Apply user-supplied stratification cutoff", "topics": [ "km_ucut" ] }, { "page": "km_val_cut", "title": "Validate stratification cutoffs on test data", "topics": [ "km_val_cut" ] }, { "page": "transpose_table", "title": "Transpose a data table", "topics": [ "transpose_table" ] }, { "page": "ucox_batch", "title": "Fit Cox regression models in batch mode", "topics": [ "ucox_batch" ] }, { "page": "ucox_pred", "title": "Fit and validate Cox regression models", "topics": [ "ucox_pred" ] } ], "_rundeps": [ "abind", "Biobase", "BiocGenerics", "codetools", "DelayedArray", "doParallel", "foreach", "generics", "GenomicRanges", "IRanges", "iterators", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "pracma", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "SummarizedExperiment", "survival", "XVector" ], "_vignettes": [ { "source": "kmcut_intro.Rmd", "filename": "kmcut_intro.html", "title": "kmcut_intro", "author": "Igor B. Kuznetsov", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Preparing the input data", "Running the package and interpreting the output", "'create_se_object'", "'km_opt_pcut'", "'km_opt_scut'", "'km_qcut'", "'km_ucut'", "'km_val_cut'", "'ucox_batch'", "'ucox_pred'", "Table manipulation", "'extract_rows'", "'extract_columns'", "'transpose_table'", "Session Information", "References" ], "created": "2023-04-20 17:50:42", "modified": "2024-04-25 03:51:19", "commits": 2 } ], "_score": 3.3010299956639813, "_indexed": false, "_nocasepkg": "kmcut", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/kmcut", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.6.0", "date": "2026-05-29T07:42:37.000Z", "distro": "noble", "commit": "5bd54fd9c0d524247dee4994fc683b957694d1be", "fileid": "acb51ae0dce40230fb924e58def01bb1678c119a8a4eb890bd7e11de369c3c6f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624618415" }, { "r": "4.6.0", "os": "linux", "version": "1.6.0", "date": "2026-05-29T07:43:41.000Z", "distro": "noble", "commit": "5bd54fd9c0d524247dee4994fc683b957694d1be", "fileid": "c9996d3ac50b1ce40528f0819e2e75bd5a08b8fe8ae07205e8ddd9a8ba9067d2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624618415" }, { "r": "4.5.3", "os": "mac", "version": "1.6.0", "date": "2026-05-29T08:48:18.000Z", "commit": "5bd54fd9c0d524247dee4994fc683b957694d1be", "fileid": "9188eb39e81f0a92344d2bf9f54c3619eb3feae64123508c39b7b632d42f526c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624618415" }, { "r": "4.6.0", "os": "mac", "version": "1.6.0", "date": "2026-05-29T08:49:01.000Z", "commit": "5bd54fd9c0d524247dee4994fc683b957694d1be", "fileid": "2339541b99cae0fe4fc0d4a4d59749be60a02903ab745f404e73ece4c6fe0103", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624618415" }, { "r": "4.6.0", "os": "wasm", "version": "1.6.0", "date": "2026-05-29T07:41:58.000Z", "commit": "5bd54fd9c0d524247dee4994fc683b957694d1be", "fileid": "85044b84132b7454abbad022a97d55db0e81691b2b63657f1ff4878dd8ec057f", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624618415" }, { "r": "4.7.0", "os": "win", "version": "1.6.0", "date": "2026-05-29T07:41:14.000Z", "commit": "5bd54fd9c0d524247dee4994fc683b957694d1be", "fileid": "4c0b2941d639ce478e40a8588faf38e2bb4267dec96a193f0c655d8f3c417385", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624618415" }, { "r": "4.5.3", "os": "win", "version": "1.6.0", "date": "2026-05-29T07:41:18.000Z", "commit": "5bd54fd9c0d524247dee4994fc683b957694d1be", "fileid": "a09dff94d95d71a5796af52cb80291da13ca3b83a27c4f652f6cb590709807fe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624618415" }, { "r": "4.6.0", "os": "win", "version": "1.6.0", "date": "2026-05-29T07:41:02.000Z", "commit": "5bd54fd9c0d524247dee4994fc683b957694d1be", "fileid": "979cb27ad53537e3a458a185d43ca23cb5273757e3b49e0dc9375241ea36c5df", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624618415" } ] }