{ "_id": "6ac20f35773a0037682c1345", "Package": "combiroc", "Title": "Selection and Ranking of Omics Biomarkers Combinations Made Easy", "Date": "2023-07-04", "Version": "0.3.4", "Language": "en-US", "Authors@R": "c(person(given = \"Ivan\",\nfamily = \"Ferrari\",\nrole = \"aut\",\nemail = \"ferrari@ingm.org\",\ncomment = c(ORCID = \"0000-0003-3746-4143\")),\nperson(given = \"Riccardo L.\",\nfamily = \"Rossi\",\nrole = c(\"aut\", \"cre\"),\nemail = \"ric.rossi@gmail.com\",\ncomment = c(ORCID = \"0000-0002-4964-3264\")),\nperson(given = \"Saveria\",\nfamily = \"Mazzara\",\nrole = \"aut\",\nemail = \"saveria.mazzara@gmail.com\",\ncomment = c(ORCID = \"0000-0003-1799-2360\")),\nperson(given = \"Mauro\",\nfamily = \"Bombaci\",\nrole = c(\"ccp\", \"ctb\", \"dtc\"),\nemail = \"bombaci@ingm.org\",\ncomment = c(ORCID = \"0000-0002-9887-4165\")))", "Description": "Provides functions and a workflow to easily and powerfully\ncalculating specificity, sensitivity and ROC curves of\nbiomarkers combinations. Allows to rank and select\nmulti-markers signatures as well as to find the best performing\nsub-signatures, now also from single-cell RNA-seq datasets. The\nmethod used was first published as a Shiny app and described in\nMazzara et al. (2017) and further\ndescribed in Bombaci & Rossi (2019)\n, and widely expanded as a\npackage as presented in the bioRxiv pre print Ferrari et al.\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "URL": "https://doi.org/10.1101/2022.01.17.476603,\nhttps://github.com/ingmbioinfo/combiroc", "BugReports": "https://github.com/ingmbioinfo/combiroc/issues", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://ingmbioinfo.r-universe.dev", "Date/Publication": "2026-01-07 10:07:34 UTC", "RemoteUrl": "https://github.com/ingmbioinfo/combiroc", "RemoteRef": "HEAD", "RemoteSha": "93c57d501a84ad20dd7e3a9ba35c6aa6bc12b4ed", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-04 08:09:56 UTC", "User": "root" }, "Author": "Ivan Ferrari [aut] (ORCID: ),\nRiccardo L. Rossi [aut, cre] (ORCID:\n),\nSaveria Mazzara [aut] (ORCID: ),\nMauro Bombaci [ccp, ctb, dtc] (ORCID:\n)", "Maintainer": "Riccardo L. Rossi ", "_user": "ingmbioinfo", "_type": "src", "_file": "combiroc_0.3.4.tar.gz", "_fileid": "https://r2.ropensci.org/d3d604c9ab2bf9092d9e5643466281e1b82c36b8f60e307666cbaf8589eea4f0", "_filesize": 8664565, "_sha256": "d3d604c9ab2bf9092d9e5643466281e1b82c36b8f60e307666cbaf8589eea4f0", "_expires": "2027-01-12T08:32:51.000Z", "_created": "2026-10-04T08:09:56.000Z", "_published": "2026-10-04T08:32:53.796Z", "_jobs": [ { "job": 111394175464, "time": 182, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11297902598" }, { "job": 111394175484, "time": 193, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11298396181" }, { "job": 111394175432, "time": 312, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11298069177" }, { "job": 111394175472, "time": 194, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11297842765" }, { "job": 111393506813, "time": 242, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "11297448384" }, { "job": 111394175402, "time": 141, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11297259558" }, { "job": 111394175467, "time": 121, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11297357343" }, { "job": 111394175504, "time": 86, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11298001305" }, { "job": 111394175471, "time": 129, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11298012231" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/ingmbioinfo/actions/runs/37187818773", "_status": "failure", "_upstream": "https://github.com/ingmbioinfo/combiroc", "_commit": { "id": "93c57d501a84ad20dd7e3a9ba35c6aa6bc12b4ed", "author": "Riccardo L. Rossi ", "committer": "GitHub ", "message": "Update README.md\n\nadded details", "time": 1767780454 }, "_maintainer": { "name": "Riccardo L. Rossi", "email": "ric.rossi@gmail.com", "login": "ricrossi", "description": "", "uuid": 3842953, "orcid": "0000-0002-4964-3264" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "tidyr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "gtools", "role": "Imports" }, { "package": "pROC", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "moments", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "httr", "role": "Suggests" }, { "package": "Seurat", "role": "Suggests" } ], "_owner": "ingmbioinfo", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-02", "n": 3 } ], "_tags": [], "_stars": 6, "_contributors": [ { "user": "ivanferrari95", "count": 10, "uuid": 72440462 }, { "user": "ricrossi", "count": 4, "uuid": 3842953 } ], "_userbio": { "uuid": 88338188, "type": "organization", "name": "Bioinformatics @ INGM Milan", "followers": 5 }, "_downloads": { "count": 421, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/combiroc" }, "_devurl": "https://github.com/ingmbioinfo/combiroc", "_searchresults": 16, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/combiroc.html", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/ingmbioinfo/combiroc", "_realowner": "ingmbioinfo", "_cranurl": true, "_releases": [ { "version": "0.2.3", "date": "2021-08-17" }, { "version": "0.3.4", "date": "2023-07-06" } ], "_exports": [ "combi", "combi_score", "combiroc_long", "combs_with", "load_data", "markers_distribution", "ranked_combs", "roc_reports", "seurat_to_combiroc", "show_markers", "single_markers_statistics" ], "_datasets": [ { "name": "demo_data", "title": "A demo dataset with proteomics markers", "object": "demo_data", "class": [ "data.frame" ], "fields": [ "Patient.ID", "Class", "Marker1", "Marker2", "Marker3", "Marker4", "Marker5" ], "rows": 170, "table": true, "tojson": true }, { "name": "demo_unclassified_data", "title": "A demo dataset with unlabeled proteomics markers", "object": "demo_unclassified_data", "class": [ "data.frame" ], "fields": [ "Patient.ID", "Marker1", "Marker2", "Marker3", "Marker4", "Marker5" ], "rows": 20, "table": true, "tojson": true } ], "_help": [ { "page": "combi", "title": "Compute combinations.", "topics": [ "combi" ] }, { "page": "combi_score", "title": "Compute the combi score using glm(link='binomial') models and optionally classifies the samples.", "topics": [ "combi_score" ] }, { "page": "combiroc_long", "title": "Reshape combiroc data in long format.", "topics": [ "combiroc_long" ] }, { "page": "combs_with", "title": "Show combinations with given markers.", "topics": [ "combs_with" ] }, { "page": "demo_data", "title": "A demo dataset with proteomics markers", "topics": [ "demo_data" ] }, { "page": "demo_unclassified_data", "title": "A demo dataset with unlabeled proteomics markers", "topics": [ "demo_unclassified_data" ] }, { "page": "load_data", "title": "Load CombiROC data.", "topics": [ "load_data" ] }, { "page": "markers_distribution", "title": "Show distribution of intensity values for all the markers both singularly and all together.", "topics": [ "markers_distribution" ] }, { "page": "ranked_combs", "title": "Rank combinations.", "topics": [ "ranked_combs" ] }, { "page": "roc_reports", "title": "Train logistic regression and compute ROC.", "topics": [ "roc_reports" ] }, { "page": "seurat_to_combiroc", "title": "Load CombiROC data.", "topics": [ "seurat_to_combiroc" ] }, { "page": "show_markers", "title": "Show the composition of combinations.", "topics": [ "show_markers" ] }, { "page": "single_markers_statistics", "title": "Provide statistics for each marker.", "topics": [ "single_markers_statistics" ] } ], "_readme": "https://github.com/ingmbioinfo/combiroc/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "gtools", "isoband", "labeling", "lifecycle", "magrittr", "moments", "pillar", "pkgconfig", "pROC", "purrr", "R6", "RColorBrewer", "Rcpp", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_score": 3.681241237375587, "_indexed": true, "_nocasepkg": "combiroc", "_universes": [ "ingmbioinfo", "ricrossi" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.4", "date": "2026-10-04T08:12:48.000Z", "distro": "resolute", "commit": "93c57d501a84ad20dd7e3a9ba35c6aa6bc12b4ed", "fileid": "https://r2.ropensci.org/6ca57c6c79aff8d7fa19dc546244e544a695823f3baab40b385499b032374427", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ingmbioinfo/actions/runs/37187818773" }, { "r": "4.6.1", "os": "linux", "version": "0.3.4", "date": "2026-10-04T08:13:01.000Z", "distro": "resolute", "commit": "93c57d501a84ad20dd7e3a9ba35c6aa6bc12b4ed", "fileid": "https://r2.ropensci.org/69fbb4f2098a64e2c5cc80412cddcb53a4d04d24e50dc00cb105b95094e88991", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ingmbioinfo/actions/runs/37187818773" }, { "r": "4.5.3", "os": "mac", "version": "0.3.4", "date": "2026-10-04T08:30:28.000Z", "commit": "93c57d501a84ad20dd7e3a9ba35c6aa6bc12b4ed", "fileid": "https://r2.ropensci.org/2956849cbeb0d5d3d7a92794f4cee6f6517f12760fda86f5c1cd893eb897c7db", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ingmbioinfo/actions/runs/37187818773" }, { "r": "4.6.1", "os": "mac", "version": "0.3.4", "date": "2026-10-04T08:27:04.000Z", "commit": "93c57d501a84ad20dd7e3a9ba35c6aa6bc12b4ed", "fileid": "https://r2.ropensci.org/e9779d3cf25a8314633f4c593060e8b58b8932cf2c78b7c92629f350f4b56d95", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ingmbioinfo/actions/runs/37187818773" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.4", "date": "2026-10-04T08:13:16.000Z", "commit": "93c57d501a84ad20dd7e3a9ba35c6aa6bc12b4ed", "fileid": "https://r2.ropensci.org/f7f5f312e4d21cf1d7490e18fb0388d0d8a72c62a322ec0a2184e0ac66e3fab7", "status": "success", "buildurl": "https://github.com/r-universe/ingmbioinfo/actions/runs/37187818773" }, { "r": "4.7.0", "os": "win", "version": "0.3.4", "date": "2026-10-04T08:11:41.000Z", "commit": "93c57d501a84ad20dd7e3a9ba35c6aa6bc12b4ed", "fileid": "https://r2.ropensci.org/c0a16cb37c75c46768c70348e5430c5a53b481895bd5c572ed310041e6ff3f46", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ingmbioinfo/actions/runs/37187818773" }, { "r": "4.5.3", "os": "win", "version": "0.3.4", "date": "2026-10-04T08:11:21.000Z", "commit": "93c57d501a84ad20dd7e3a9ba35c6aa6bc12b4ed", "fileid": "https://r2.ropensci.org/96dc77d62b185a993dca08b700569dbb0750dc3061de49463cc9f42c7a468ccf", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ingmbioinfo/actions/runs/37187818773" }, { "r": "4.6.1", "os": "win", "version": "0.3.4", "date": "2026-10-04T08:11:52.000Z", "commit": "93c57d501a84ad20dd7e3a9ba35c6aa6bc12b4ed", "fileid": "https://r2.ropensci.org/c8479d02ae872d6dfa7c95beac17c8d445c4e1b18e0818ad7724fb422ed33a80", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ingmbioinfo/actions/runs/37187818773" } ] }