{ "_id": "6a2270dccd65a98ecbd48b12", "Package": "BreastSubtypeR", "Type": "Package", "Title": "Cohort-aware methods for intrinsic molecular subtyping of breast\ncancer", "Description": "BreastSubtypeR provides an assumption-aware, multi-method\nframework for intrinsic molecular subtyping of breast cancer.\nThe package harmonizes several published nearest-centroid (NC)\nand single-sample predictor (SSP) classifiers, supplies\nmethod-specific preprocessing and robust probe-to-gene mapping,\nand implements a cohort-aware AUTO mode that selectively\nenables classifiers compatible with the cohort composition. A\nlocal Shiny app (iBreastSubtypeR) is included for interactive\nanalyses and to support users without programming experience.", "Encoding": "UTF-8", "Version": "1.4.0", "biocViews": "RNASeq, Software, GeneExpression, Classification,\nPreprocessing, Visualization", "Authors@R": "c(\nperson(given = \"Qiao\", family = \"Yang\",\nrole = c(\"aut\", \"cre\"),\nemail=\"yq.kiuo@gmail.com\",\ncomment = c(ORCID = \"0000-0002-4098-3246\")),\nperson(given = \"Emmanouil G.\", family = \"Sifakis\",\nrole = c(\"aut\"),\nemail = \"emmanouil.sifakis@ki.se\",\ncomment = c(ORCID = \"0000-0001-9919-4471\"))\n)", "URL": "https://doi.org/10.18129/B9.bioc.BreastSubtypeR,https://github.com/yqkiuo/BreastSubtypeR,https://github.com/JohanHartmanGroupBioteam/BreastSubtypeR", "BugReports": "https://github.com/yqkiuo/BreastSubtypeR/issues", "License": "GPL-3", "VignetteBuilder": "knitr", "Roxygen": "list(markdown = TRUE, roclets = c(\"rd\", \"namespace\",\n\"collate\"))", "LazyData": "FALSE", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libicu-dev libpng-dev perl zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:04:57 UTC", "RemoteUrl": "https://github.com/bioc/BreastSubtypeR", "RemoteRef": "RELEASE_3_23", "RemoteSha": "f7156aeb588fff4fb39a90b4236d11dcccb6e68d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 06:40:01 UTC", "User": "root" }, "Author": "Qiao Yang [aut, cre] (ORCID: ),\nEmmanouil G. Sifakis [aut] (ORCID:\n)", "Maintainer": "Qiao Yang ", "MD5sum": "577e7eb021f0564a7a8901cbb0a4cecf", "_user": "bioc-release", "_type": "src", "_file": "BreastSubtypeR_1.4.0.tar.gz", "_fileid": "18bbbb15c744fb4345e19d284ab99c0bde94160e290ca2f93246addcf8e3e14a", "_filesize": 6895208, "_sha256": "18bbbb15c744fb4345e19d284ab99c0bde94160e290ca2f93246addcf8e3e14a", "_created": "2026-06-05T06:40:01.000Z", "_published": "2026-06-05T06:46:52.767Z", "_jobs": [ { "job": 79677442231, "time": 167, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7430447041" }, { "job": 79677442277, "time": 342, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7430489120" }, { "job": 79677442256, "time": 348, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7430490577" }, { "job": 79677442239, "time": 220, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7430459751" }, { "job": 79677442266, "time": 226, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7430460879" }, { "job": 79676902029, "time": 272, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7430407106" }, { "job": 79677442303, "time": 165, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7430446298" }, { "job": 79677442287, "time": 297, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7430478301" }, { "job": 79677442270, "time": 252, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7430467786" }, { "job": 79677442248, "time": 253, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7430467192" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26999619194", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/BreastSubtypeR", "_commit": { "id": "f7156aeb588fff4fb39a90b4236d11dcccb6e68d", "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": 1777381497 }, "_maintainer": { "name": "Qiao Yang", "email": "yq.kiuo@gmail.com", "login": "yqkiuo", "orcid": "0000-0002-4098-3246", "description": "Bioinformatic PhD student at Karolinska Institutet | Bioinformatic MSc in Sichuan University | BENG in Hangzhou Dianzi University", "uuid": 44391853 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "withr", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Imports" }, { "package": "impute", "version": ">= 1.80.0", "role": "Imports" }, { "package": "data.table", "version": ">= 1.16.0", "role": "Imports" }, { "package": "RColorBrewer", "version": ">= 1.1-3", "role": "Imports" }, { "package": "circlize", "version": ">= 0.4.16", "role": "Imports" }, { "package": "ggrepel", "version": ">= 0.9.6", "role": "Imports" }, { "package": "e1071", "version": ">= 1.7-8", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "lifecycle", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" }, { "package": "shiny", "version": ">= 1.9.1", "role": "Suggests" }, { "package": "bslib", "version": ">= 0.8.0", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-26", "n": 3 }, { "week": "2025-29", "n": 3 }, { "week": "2025-37", "n": 1 }, { "week": "2025-39", "n": 1 }, { "week": "2025-40", "n": 1 }, { "week": "2025-41", "n": 3 }, { "week": "2025-47", "n": 2 }, { "week": "2025-51", "n": 1 }, { "week": "2026-08", "n": 1 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.5.0", "bioc": "3.24" }, { "branch": "release", "version": "1.4.0", "bioc": "3.23" } ], "_topics": [ "rnaseq", "software", "geneexpression", "classification", "preprocessing", "visualization" ], "_stars": 4, "_contributors": [ { "user": "yqkiuo", "count": 410, "uuid": 44391853 }, { "user": "sifakise", "count": 139, "uuid": 29406706 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 254, "source": "https://www.bioconductor.org/packages/stats/bioc/BreastSubtypeR" }, "_devurl": "https://github.com/yqkiuo/breastsubtyper", "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/BreastSubtypeR.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/yqkiuo/breastsubtyper", "_realowner": "bioc", "_cranurl": false, "_exports": [ "BS_AIMS", "BS_cIHC", "BS_cIHC.itr", "BS_Multi", "BS_parker", "BS_PCAPAM50", "BS_ssBC", "BS_sspbc", "iBreastSubtypeR", "Mapping", "Vis_boxplot", "Vis_heatmap", "Vis_Multi", "Vis_PCA", "Vis_pie" ], "_datasets": [ { "name": "AIMSmodel", "title": "AIMSmodel: Model object for AIMS", "object": "AIMSmodel", "file": "AIMSmodel.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "BreastSubtypeRobj", "title": "BreastSubtypeRobj: Resources for NC-based methods", "object": "BreastSubtypeRobj", "file": "BreastSubtypeRobj.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "Gene.ID.ann", "title": "Gene.ID.ann: Gene annotation table", "object": "Gene.ID.ann", "file": "Gene.ID.ann.RData", "class": [ "data.frame" ], "fields": [ "Gene.ID", "Gene.Name", "HGNC", "EntrezGene", "RefSeq", "transcript_id" ], "rows": 19675, "table": true, "tojson": true }, { "name": "OSLO2EMIT0obj", "title": "OSLO2EMIT0obj: Example dataset (OSLO2-EMIT0 cohort subset)", "object": "OSLO2EMIT0obj", "file": "OSLO2EMIT0obj.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "sspbc.models", "title": "sspbc.models: Short names for 11 SSPBC predictors", "object": "sspbc.models", "file": "sspbc.models.fullname.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "sspbc.models.fullname", "title": "sspbc.models.fullname: Full names for 11 SSPBC predictors", "object": "sspbc.models.fullname", "file": "sspbc.models.fullname.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "TCGABRCAobj", "title": "TCGABRCAobj: Example dataset (TCGA-BRCA subset)", "object": "TCGABRCAobj", "file": "TCGABRCAobj.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "AIMSmodel", "title": "AIMSmodel: Model object for AIMS", "topics": [ "AIMSmodel" ] }, { "page": "BreastSubtypeR", "title": "BreastSubtypeR: A Unified R/Bioconductor Package for Intrinsic Molecular Subtyping in Breast Cancer Research", "topics": [ "BreastSubtypeR-package", "BreastSubtypeR" ] }, { "page": "BreastSubtypeRobj", "title": "BreastSubtypeRobj: Resources for NC-based methods", "topics": [ "BreastSubtypeRobj" ] }, { "page": "BS_AIMS", "title": "AIMS Intrinsic Subtyping (BS_AIMS)", "topics": [ "BS_AIMS" ] }, { "page": "BS_cIHC", "title": "Conventional IHC Intrinsic Subtyping (BS_cIHC)", "topics": [ "BS_cIHC" ] }, { "page": "BS_cIHC.itr", "title": "Iterative Conventional IHC Intrinsic Subtyping (BS_cIHC.itr)", "topics": [ "BS_cIHC.itr" ] }, { "page": "BS_Multi", "title": "Intrinsic Subtyping with Multiple Approaches (BS_Multi)", "topics": [ "BS_Multi" ] }, { "page": "BS_parker", "title": "Original Parker Intrinsic Subtyping (BS_parker)", "topics": [ "BS_parker" ] }, { "page": "BS_PCAPAM50", "title": "PCA-PAM50 Intrinsic Subtyping (BS_PCAPAM50)", "topics": [ "BS_PCAPAM50" ] }, { "page": "BS_ssBC", "title": "Subgroup-Specific Gene-Centering Intrinsic Subtyping (BS_ssBC)", "topics": [ "BS_ssBC" ] }, { "page": "BS_sspbc", "title": "Intrinsic Subtyping using SSPBC (BS_sspbc)", "topics": [ "BS_sspbc" ] }, { "page": "Gene.ID.ann", "title": "Gene.ID.ann: Gene annotation table", "topics": [ "Gene.ID.ann" ] }, { "page": "iBreastSubtypeR", "title": "Launch the iBreastSubtypeR Shiny app", "topics": [ "iBreastSubtypeR" ] }, { "page": "Mapping", "title": "Gene ID Mapping", "topics": [ "Mapping" ] }, { "page": "OSLO2EMIT0obj", "title": "OSLO2EMIT0obj: Example dataset (OSLO2-EMIT0 cohort subset)", "topics": [ "OSLO2EMIT0obj" ] }, { "page": "sspbc.models", "title": "sspbc.models: Short names for 11 SSPBC predictors", "topics": [ "sspbc.models" ] }, { "page": "sspbc.models.fullname", "title": "sspbc.models.fullname: Full names for 11 SSPBC predictors", "topics": [ "sspbc.models.fullname" ] }, { "page": "TCGABRCAobj", "title": "TCGABRCAobj: Example dataset (TCGA-BRCA subset)", "topics": [ "TCGABRCAobj" ] }, { "page": "Vis_boxplot", "title": "Boxplot of Correlation per Subtype", "topics": [ "Vis_boxplot" ] }, { "page": "Vis_heatmap", "title": "Heatmap Visualization of Gene Expression by Subtype", "topics": [ "Vis_heatmap" ] }, { "page": "Vis_Multi", "title": "Multi-Method Subtype Heatmap Visualization", "topics": [ "Vis_Multi" ] }, { "page": "Vis_PCA", "title": "PCA Plot Visualization of Gene Expression by Subtype", "topics": [ "Vis_PCA" ] }, { "page": "Vis_pie", "title": "Pie Chart Visualization of Subtype Distribution", "topics": [ "Vis_pie" ] } ], "_readme": "https://github.com/bioc/BreastSubtypeR/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "circlize", "class", "cli", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "cpp11", "crayon", "data.table", "DelayedArray", "digest", "doParallel", "dplyr", "e1071", "edgeR", "farver", "foreach", "generics", "GenomicRanges", "GetoptLong", "ggplot2", "ggrepel", "GlobalOptions", "glue", "gtable", "impute", "IRanges", "isoband", "iterators", "labeling", "lattice", "lifecycle", "limma", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "pillar", "pkgconfig", "png", "proxy", "R6", "RColorBrewer", "Rcpp", "rjson", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "shape", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "BreastSubtypeR.Rmd", "filename": "BreastSubtypeR.html", "title": "BreastSubtypeR: Introduction and Workflow", "author": "Qiao Yang, Emmanouil G. Sifakis", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Citing BreastSubtypeR", "Brief description", "Features", "Implemented approaches", "Quick start", "Guidance & best practices", "Input types", "When to use AUTO", "Interpretation", "Shiny app", "Launch the local Shiny app", "Example data (for Shiny & scripts)", "Limitations", "Appendix", "Sources & support", "References", "Session information" ], "created": "2024-12-17 23:12:55", "modified": "2025-11-23 09:09:22", "commits": 32 } ], "_score": 5.342422680822207, "_indexed": false, "_nocasepkg": "breastsubtyper", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/BreastSubtypeR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4.0", "date": "2026-06-05T06:43:52.000Z", "distro": "noble", "commit": "f7156aeb588fff4fb39a90b4236d11dcccb6e68d", "fileid": "06eb0ebe85aac6f7c72dec5086fca08bd380d840c2ce90ba50b28041896b5e89", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26999619194" }, { "r": "4.6.0", "os": "linux", "version": "1.4.0", "date": "2026-06-05T06:43:42.000Z", "distro": "noble", "commit": "f7156aeb588fff4fb39a90b4236d11dcccb6e68d", "fileid": "03bc14ddaa0585ba616dfd90cd296dbc2ac951f45d44473cdcd2b938ef891ddc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26999619194" }, { "r": "4.5.3", "os": "mac", "version": "1.4.0", "date": "2026-06-05T06:42:22.000Z", "commit": "f7156aeb588fff4fb39a90b4236d11dcccb6e68d", "fileid": "a063f8fb2e9947b4c3171423c3b97d01a3d3cfd043cf5eedbcf398c986f501fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26999619194" }, { "r": "4.6.0", "os": "mac", "version": "1.4.0", "date": "2026-06-05T06:42:22.000Z", "commit": "f7156aeb588fff4fb39a90b4236d11dcccb6e68d", "fileid": "856461593129db987a2f055b189790a936767a0e61ea5c631ea37e4980499efc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26999619194" }, { "r": "4.6.0", "os": "wasm", "version": "1.4.0", "date": "2026-06-05T06:43:20.000Z", "commit": "f7156aeb588fff4fb39a90b4236d11dcccb6e68d", "fileid": "4eb8ad186ef9cd30e5e255f6f644348859b1385a9187c514048f99115b3b385d", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26999619194" }, { "r": "4.7.0", "os": "win", "version": "1.4.0", "date": "2026-06-05T06:42:49.000Z", "commit": "f7156aeb588fff4fb39a90b4236d11dcccb6e68d", "fileid": "ed5e6245965e30047c8851595422ad0f58bf3c6cd77e17a68be229cabc4ca9a6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26999619194" }, { "r": "4.5.3", "os": "win", "version": "1.4.0", "date": "2026-06-05T06:42:07.000Z", "commit": "f7156aeb588fff4fb39a90b4236d11dcccb6e68d", "fileid": "9d8b61d8bf4c3e819801f6fb06aa63e0ee06885608ad69957d867babf0ce0669", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26999619194" }, { "r": "4.6.0", "os": "win", "version": "1.4.0", "date": "2026-06-05T06:41:56.000Z", "commit": "f7156aeb588fff4fb39a90b4236d11dcccb6e68d", "fileid": "b324b5818bf0e30ee0a6fcd813ca499418757a0c7b191d963330a864914a4347", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26999619194" } ] }