{ "_id": "6ad2b9c56814ce853b657b3b", "Package": "thyroidBRS", "Title": "BRAF-RAS Score (BRS) Classifier for Papillary Thyroid Carcinoma", "Version": "0.99.8", "Authors@R": "c(\nperson(\"Camila\", \"Barrios-Cervantes\",\nemail = \"paulacamilabarrioscervantes@gmail.com\",\nrole = c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0009-0006-9971-790X\")),\nperson(\"Daniel\", \"Pérez-Calixto\",\nemail = \"daniel_perez@ciencias.unam.mx\",\nrole = c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0009-0004-3988-1260\")),\nperson(\"Hugo\", \"Tovar\",\nemail = \"hatovar@inmegen.gob.mx\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-8360-6133\")),\nperson(\"Instituto Nacional de Medicina Genómica\", role = \"fnd\",\ncomment = c(ROR = \"https://ror.org/01qjckx08\",\nproject = \"INMEGEN-2026-14 (Proyecto 81)\")))", "Description": "Computes the BRAF-RAS Score (BRS), a 71-gene\nexpression-based signature that quantifies whether a papillary\nthyroid carcinoma (PTC) sample resembles a BRAF-V600E-mutant or\na RAS-mutant transcriptional profile, following Agrawal et al.\n(2014) , Extended Experimental\nProcedures, section 14.1. It is a re-implementation from that\ndescription rather than the original code, which was never\nreleased: it reproduces the published classification (99.7\npercent against driver-mutation status under cross-validation)\nbut not the exact published score values. The original study\nonly scored the subset of samples for which both exome and RNA\nsequencing data were available, since exome data was needed to\ndefine the two reference groups (but not to score additional\nsamples). This package lets you fit the reference centroids\nfrom any cohort with known BRAF-mutant/RAS-mutant labels and\nthen score new samples — including ones with expression data\nonly — using just their gene expression. Expression can be\nsupplied as a matrix, a SummarizedExperiment or an\nExpressionSet.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "biocViews": "Software, Classification, DriverMutation, GeneExpression,\nTranscriptomics, RNASeq, Microarray, Sequencing,\nBiomedicalInformatics", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "URL": "https://github.com/camilasauria/thyroidBRS", "BugReports": "https://github.com/camilasauria/thyroidBRS/issues", "Config/roxygen2/version": "8.1.0", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-10-16 18:00:32 UTC", "RemoteUrl": "https://github.com/bioc/thyroidBRS", "RemoteRef": "HEAD", "RemoteSha": "b05a43b5dbe986c9ef2bfeff4eab0b18f5a4b543", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-16 23:51:00 UTC", "User": "root" }, "Author": "Camila Barrios-Cervantes [aut, cph] (ORCID:\n),\nDaniel Pérez-Calixto [aut, cph] (ORCID:\n),\nHugo Tovar [aut, cre, cph] (ORCID:\n),\nInstituto Nacional de Medicina Genómica [fnd] (ROR:\n, project: INMEGEN-2026-14 (Proyecto\n81))", "Maintainer": "Hugo Tovar ", "_user": "bioc", "_type": "src", "_file": "thyroidBRS_0.99.8.tar.gz", "_fileid": "https://r2.ropensci.org/92f95fa9150c7d6280c0a9b064cb732268680fa756f9d6f32e7f99f4a19bb8c2", "_filesize": 242609, "_sha256": "92f95fa9150c7d6280c0a9b064cb732268680fa756f9d6f32e7f99f4a19bb8c2", "_expires": "2027-01-24T23:56:51.000Z", "_created": "2026-10-16T23:51:00.000Z", "_published": "2026-10-16T23:56:53.773Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38983257098", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 2 }, "_upstream": "https://github.com/bioc/thyroidBRS", "_commit": { "id": "b05a43b5dbe986c9ef2bfeff4eab0b18f5a4b543", "author": "Camila Barrios <151900030+camilasauria@users.noreply.github.com>", "committer": "GitHub ", "message": "Merge pull request #4 from camilasauria/bioc-zenodo-badges\n\nAdd Bioconductor and Zenodo badges, cite the Zenodo DOI (0.99.8)", "time": 1792173632 }, "_maintainer": { "name": "Hugo Tovar", "email": "hatovar@inmegen.gob.mx", "login": "hachepunto", "orcid": "0000-0002-8360-6133", "twitter": "@geekbiology", "description": "", "uuid": 6043622 }, "_distro": "resolute", "_jobs": [ { "job": 117249834871, "time": 156, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "12081563521" }, { "job": 117249835692, "time": 235, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12081749662" }, { "job": 117249834898, "time": 305, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12082261815" }, { "job": 117249834857, "time": 121, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12082546228" }, { "job": 117249834913, "time": 196, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12081828797" }, 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