{ "_id": "6a4b4546a6574ff277f98bce", "Package": "iPath", "Type": "Package", "Title": "iPath pipeline for detecting perturbed pathways at individual\nlevel", "Version": "1.19.0", "Authors@R": "c(person(\"Kenong\",\"Su\", email =\"kenong.su@emory.edu\", role = c(\"aut\",\"cre\")),\nperson(\"Zhaohui\",\"Qin\", email =\"zhaohui.qin@emory.edu\", role =\"aut\"))", "Description": "iPath is the Bioconductor package used for calculating\npersonalized pathway score and test the association with\nsurvival outcomes. Abundant single-gene biomarkers have been\nidentified and used in the clinics. However, hundreds of\noncogenes or tumor-suppressor genes are involved during the\nprocess of tumorigenesis. We believe individual-level\nexpression patterns of pre-defined pathways or gene sets are\nbetter biomarkers than single genes. In this study, we devised\na computational method named iPath to identify prognostic\nbiomarker pathways, one sample at a time. To test its utility,\nwe conducted a pan-cancer analysis across 14 cancer types from\nThe Cancer Genome Atlas and demonstrated that iPath is capable\nof identifying highly predictive biomarkers for clinical\noutcomes, including overall survival, tumor subtypes, and tumor\nstage classifications. We found that pathway-based biomarkers\nare more robust and effective than single genes.", "License": "GPL-2", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "biocViews": "Pathways, Software, GeneExpression, Survival", "NeedsCompilation": "yes", "SystemRequirements": "C++11", "RoxygenNote": "7.1.1", "BugReports": "https://github.com/suke18/iPath/issues", "Config/pak/sysreqs": "cmake make libicu-dev libjpeg-dev libpng-dev\nlibxml2-dev libssl-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:56:34 UTC", "RemoteUrl": "https://github.com/bioc/iPath", "RemoteRef": "HEAD", "RemoteSha": "a1baeabb37f526ef5c0f4f55d2f146a88c789dcd", "Packaged": { "Date": "2026-07-04 04:10:50 UTC", "User": "root" }, "Author": "Kenong Su [aut, cre],\nZhaohui Qin [aut]", "Maintainer": "Kenong Su ", "_user": "bioc", "_type": "src", "_file": "iPath_1.19.0.tar.gz", "_fileid": "https://r2.ropensci.org/afef93b5aab3bb26b425d94faa5c91ec76c91cb3965d4f5925937b972ae25a01", "_filesize": 2948592, "_sha256": "afef93b5aab3bb26b425d94faa5c91ec76c91cb3965d4f5925937b972ae25a01", "_expires": "2026-10-12T17:14:32.000Z", "_created": "2026-07-04T04:10:50.000Z", "_published": "2026-07-06T06:03:50.380Z", "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28694381432", "_status": "success", "_upstream": "https://github.com/bioc/iPath", "_commit": { "id": "a1baeabb37f526ef5c0f4f55d2f146a88c789dcd", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380994 }, "_maintainer": { "name": "Kenong Su", "email": "kenong.su@emory.edu" }, "_distro": "resolute", "_jobs": [ { "job": 85304642666, "time": 177, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8078187681" }, { "job": 85304642843, "time": 281, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "8078200411" }, { "job": 85304642688, "time": 302, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8078202373" }, { "job": 85304642709, "time": 293, "config": "linux-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8078201727" }, { "job": 85304642924, "time": 303, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8078202561" }, { "job": 85304642252, "time": 79, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 85304642274, "time": 222, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 85304642560, "time": 189, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8078717075" }, { "job": 85304642611, "time": 268, "config": "macos-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8078198463" }, { "job": 85304642171, "time": 314, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8078165594" }, { "job": 85304642753, "time": 193, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8078189320" }, { "job": 85304642168, "time": 244, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "8100875471" }, { "job": 85304642141, "time": 90, "config": "windows-oldrel", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 85304642139, "time": 224, "config": "windows-release", "r": "4.6.1", "check": "ERROR", "artifact": "8100873383" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "mclust", "role": "Depends" }, { "package": "BiocParallel", "role": "Depends" }, { "package": "survival", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.5", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "ggpubr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "survminer", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "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": [ "pathways", "software", "geneexpression", "survival", "cpp" ], "_stars": 2, "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 95, "_devurl": "https://github.com/suke18/ipath", "_searchresults": 5, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/iPath.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_homeurl": "https://github.com/suke18/ipath", "_realowner": "bioc", "_cranurl": false, "_exports": [ "density_fall", "iES_cal2", "iES_surv", "iES_survPlot", "water_fall" ], "_datasets": [ { "name": "GSDB_example", "title": "example gene set database (GSDB)", "object": "GSDB_example", "file": "GSDB_example.RData", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "prad_cli", "title": "simulated clinical data for PRAD cancer patients", "object": "PRAD_data", "file": "PRAD_data.RData", "class": [ "data.frame" ], "fields": [ "times", "bcr_patient_barcode", "patient.vital_status" ], "rows": 499, "table": true, "tojson": true }, { "name": "prad_exprs", "title": "expression matrix for PRAD cancer patients in TCGA", "object": "PRAD_data", "file": "PRAD_data.RData", "class": [ "matrix", "array" ], "fields": [ "TCGA-VP-A87C", "TCGA-G9-7525", "TCGA-CH-5739", "TCGA-HC-7231", "TCGA-XJ-A83F", "TCGA-KK-A59Y", "TCGA-EJ-A65D", "TCGA-KC-A7F5", "TCGA-HC-8259", "TCGA-HC-A6AO", "TCGA-XQ-A8TA", "TCGA-V1-A8WL", "TCGA-G9-6354", "TCGA-EJ-7785", "TCGA-HC-A9TH", "TCGA-HC-7233", "TCGA-XJ-A9DQ", "TCGA-KK-A8IM", "TCGA-FC-A66V", "TCGA-M7-A724", "TCGA-KK-A7B2", "TCGA-CH-5754", "TCGA-2A-A8W3", "TCGA-XK-AAJU", "TCGA-HC-A8D1", "TCGA-HC-7747", "TCGA-EJ-7325", "TCGA-EJ-7331", "TCGA-CH-5794", "TCGA-QU-A6IM", "TCGA-V1-A8MU", "TCGA-KK-A8I5", "TCGA-G9-6338", "TCGA-CH-5768", "TCGA-EJ-8474", "TCGA-J4-A67K", "TCGA-V1-A9Z8", "TCGA-KK-A7B4", "TCGA-CH-5751", "TCGA-KK-A6DY", "TCGA-FC-A4JI", "TCGA-VN-A88P", "TCGA-HC-8216", "TCGA-G9-6370", "TCGA-HC-7817", "TCGA-J9-A8CL", "TCGA-EJ-5522", "TCGA-EJ-5526", "TCGA-EJ-7125", "TCGA-CH-5761", "TCGA-CH-5766", "TCGA-CH-5767", "TCGA-EJ-5530", "TCGA-EJ-5531", "TCGA-EJ-5532", "TCGA-EJ-7115", "TCGA-EJ-7123", "TCGA-EJ-7312", "TCGA-EJ-7314", "TCGA-EJ-7315", "TCGA-EJ-7317", "TCGA-EJ-7318", "TCGA-EJ-7321", "TCGA-EJ-7327", "TCGA-EJ-7328", "TCGA-EJ-7330", "TCGA-EJ-8472", "TCGA-EJ-A65M", "TCGA-EJ-A7NG", "TCGA-EJ-A7NK", "TCGA-EJ-A7NM", "TCGA-EJ-A8FO", "TCGA-EJ-A8FP", "TCGA-EJ-A8FS", "TCGA-EJ-AB20", "TCGA-G9-6332", "TCGA-G9-6336", "TCGA-G9-6339", "TCGA-G9-6367", "TCGA-G9-6384", "TCGA-G9-6385", "TCGA-G9-6494", "TCGA-G9-6496", "TCGA-G9-6498", "TCGA-G9-7510", "TCGA-G9-7522", "TCGA-H9-A6BX", "TCGA-H9-A6BY", "TCGA-HC-7075", "TCGA-HC-7078", "TCGA-HC-8257" ], "rows": 10000, "table": true, "tojson": true }, { "name": "prad_inds", "title": "normal (0) and tumor (1) classes associated with PRAD expression data", "object": "PRAD_data", "file": "PRAD_data.RData", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "density_fall", "title": "density fall plot", "topics": [ "density_fall" ] }, { "page": "GSDB_example", "title": "example gene set database (GSDB)", "topics": [ "GSDB_example" ] }, { "page": "GSEA", "title": "GSEA calculation", "topics": [ "GSEA" ] }, { "page": "iES_cal2", "title": "iES calculation Function", "topics": [ "iES_cal2" ] }, { "page": "iES_surv", "title": "iES calculation Function", "topics": [ "iES_surv" ] }, { "page": "iES_survPlot", "title": "iES survival for a certain pathway", "topics": [ "iES_survPlot" ] }, { "page": "prad_cli", "title": "simulated clinical data for PRAD cancer patients", "topics": [ "prad_cli" ] }, { "page": "prad_exprs", "title": "expression matrix for PRAD cancer patients in TCGA", "topics": [ "prad_exprs" ] }, { "page": "prad_inds", "title": "normal (0) and tumor (1) classes associated with PRAD expression data", "topics": [ "prad_inds" ] }, { "page": "rem_data", "title": "remove genes with 0 sd", "topics": [ "rem_data" ] }, { "page": "setUp_BPPARAM", "title": "set up for the parallel computing for biocParallel.", "topics": [ "setUp_BPPARAM" ] }, { "page": "water_fall", "title": "water fall plot", "topics": [ "water_fall" ] } ], "_rundeps": [ "abind", "backports", "BH", "BiocParallel", "boot", "broom", "car", "carData", "cli", "codetools", "colorspace", "commonmark", "corrplot", "cowplot", "cpp11", "curl", "Deriv", "doBy", "dplyr", "exactRankTests", "farver", "forecast", "formatR", "Formula", "fracdiff", "futile.logger", "futile.options", "generics", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "ggtext", "glue", "gridExtra", "gridtext", "gtable", "isoband", "jpeg", "labeling", "lambda.r", "lattice", "lifecycle", "litedown", "lme4", "lmtest", "magrittr", "markdown", "MASS", "Matrix", "MatrixModels", "matrixStats", "maxstat", "mclust", "mgcv", "minqa", "modelr", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "pbkrtest", "pillar", "pkgconfig", "png", "polynom", "purrr", "quantreg", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "rlang", "rstatix", "S7", "scales", "snow", "SparseM", "stringi", "stringr", "survival", "survminer", "tibble", "tidyr", "tidyselect", "timeDate", "urca", "utf8", "vctrs", "viridisLite", "withr", "xfun", "xml2", "zoo" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "iPath.Rmd", "filename": "iPath.html", "title": "The iPath User's Guide", "author": "Kenong Su, Steve Qin", "engine": "knitr::rmarkdown", "headings": [ "Installation and help", "Install iPath", "Help for iPath", "Introduction", "Background", "Citation", "Calculate iES", "Load the data", "Calculate iES per sample per pathway", "Test association with survival outcomes", "Data visualization", "waterfall", "one survival outcomes", "Session Info" ], "created": "2021-06-25 02:19:13", "modified": "2021-06-25 02:19:13", "commits": 1 } ], "_score": 4.6020599913279625, "_indexed": true, "_nocasepkg": "ipath", "_universes": [ "bioc", "suke18" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-07-04T04:14:56.000Z", "distro": "resolute", "arch": "aarch64", "commit": "a1baeabb37f526ef5c0f4f55d2f146a88c789dcd", "fileid": "https://r2.ropensci.org/5a681e72e5dbbb26d776cb7dd9245dd66306eb37915a9dbc6e34f773a58b9454", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694381432" }, { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-07-04T04:14:50.000Z", "distro": "resolute", "arch": "x86_64", "commit": "a1baeabb37f526ef5c0f4f55d2f146a88c789dcd", "fileid": "https://r2.ropensci.org/1c735dba59d2c109a5562c0a9d5343c421c04970e7950b33f456ae5c354fd97b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694381432" }, { "r": "4.6.1", "os": "linux", "version": "1.19.0", "date": "2026-07-04T04:15:08.000Z", "distro": "resolute", "arch": "aarch64", "commit": "a1baeabb37f526ef5c0f4f55d2f146a88c789dcd", "fileid": "https://r2.ropensci.org/92f8179f6cbaf4cc3323b0586a9deda832c58dc6816664c59670dad1decdea83", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694381432" }, { "r": "4.6.1", "os": "linux", "version": "1.19.0", "date": "2026-07-04T04:14:47.000Z", "distro": "resolute", "arch": "x86_64", "commit": "a1baeabb37f526ef5c0f4f55d2f146a88c789dcd", "fileid": "https://r2.ropensci.org/4b3a1b67e36c3e854b2a50dc9429916bf50c3987f137fadc70f3cf020298f876", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694381432" }, { "r": "4.6.1", "os": "mac", "version": "1.19.0", "date": "2026-07-04T05:33:03.000Z", "arch": "aarch64", "commit": "a1baeabb37f526ef5c0f4f55d2f146a88c789dcd", "fileid": "https://r2.ropensci.org/43b12dfba79579e78c65862713b4aa998fc993872db03567d99ec19b2db7b221", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694381432" }, { "r": "4.6.1", "os": "mac", "version": "1.19.0", "date": "2026-07-04T04:13:49.000Z", "arch": "x86_64", "commit": "a1baeabb37f526ef5c0f4f55d2f146a88c789dcd", "fileid": "https://r2.ropensci.org/8c027a308a3ecf2f05c8a33d040d18ef1bef8bc7e02f78e13183d6bc7f8b7845", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694381432" }, { "r": "4.6.0", "os": "wasm", "version": "1.19.0", "date": "2026-07-04T04:14:24.000Z", "arch": "emscripten", "commit": "a1baeabb37f526ef5c0f4f55d2f146a88c789dcd", "fileid": "https://r2.ropensci.org/710ef009d135e1eb2bd4f6b7dc74436068090aae0249d1df8081f555626c41a3", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694381432" }, { "r": "4.7.0", "os": "win", "version": "1.19.0", "date": "2026-07-06T06:00:49.000Z", "arch": "x86_64", "commit": "a1baeabb37f526ef5c0f4f55d2f146a88c789dcd", "fileid": "https://r2.ropensci.org/123aaf67ced6ca1fa6311ab5419c239e8d05d21dfe0782096d02b760e99613a4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694381432" }, { "r": "4.6.1", "os": "win", "version": "1.19.0", "date": "2026-07-06T06:00:47.000Z", "arch": "x86_64", "commit": "a1baeabb37f526ef5c0f4f55d2f146a88c789dcd", "fileid": "https://r2.ropensci.org/2767f5228714827240701fbef966fd7c3a37da45bb2f646727a867e8deca093f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694381432" } ] }