{ "_id": "6a42d1354ba05a737d8b200b", "Package": "oncoPredict", "Type": "Package", "Title": "Drug Response Modeling and Biomarker Discovery", "Version": "1.3.1", "URL": "https://github.com/HuangLabUMN/oncoPredict", "BugReports": "https://github.com/HuangLabUMN/oncoPredict/issues", "Authors@R": "c(\nperson(given = 'Robert',\nfamily = 'Gruener',\nrole = c(\"aut\", \"cre\"),\nemail = 'rgruener@umn.edu',\ncomment = c(ORCID = \"0000-0002-8166-2772\")),\nperson(given = \"Danielle\",\nfamily = \"Maeser\",\nrole = \"aut\",\nemail = \"maese005@umn.edu\",\ncomment = c(ORCID = \"0000-0002-3890-887X\")))", "Maintainer": "Robert Gruener ", "Description": "Allows for building drug response models using screening\ndata between bulk RNA-Seq and a drug response metric and two\nadditional tools for biomarker discovery that have been\ndeveloped by the Huang Laboratory at University of Minnesota.\nThere are 3 main functions within this package. (1)\ncalcPhenotype() is used to build drug response models on\nRNA-Seq data and impute them on any other RNA-Seq dataset given\nto the model. (2) GLDS() is used to calculate the general level\nof drug sensitivity, which can improve biomarker discovery. (3)\nIDWAS() can take the results from calcPhenotype() and link the\nimputed response back to available genomic (mutation and CNV\nalterations) to identify biomarkers. Each of these functions\ncomes from a paper from the Huang research laboratory. Below\ngives the relevant paper for each function. The package is\ndescribed in Maeser et al. (2021) \"oncoPredict: an R package\nfor predicting in vivo or cancer patient drug response and\nbiomarkers from cell line screening data\"\n. calcPhenotype() - Geeleher et al,\nClinical drug response can be predicted using baseline gene\nexpression levels and in vitro drug sensitivity in cell lines.\nGLDS() - Geeleher et al, Cancer biomarker discovery is improved\nby accounting for variability in general levels of drug\nsensitivity in pre-clinical models. IDWAS() - Geeleher et al,\nDiscovering novel pharmacogenomic biomarkers by imputing drug\nresponse in cancer patients from large genomics studies.", "License": "GPL-2", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "biocViews": "sva, limma, stringr, biomaRt, genefilter, GenomicFeatures,\ngenefilter, TCGAbiolinks, BiocGenerics, GenomicRanges, IRanges,\nS4Vectors", "Additional_repositories": "https://bioconductor.org/packages/release/data/annotation", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-29 20:02:11 UTC", "User": "root" }, "Author": "Robert Gruener [aut, cre] (ORCID:\n), Danielle Maeser [aut]\n(ORCID: )", "Config/pak/sysreqs": "libbz2-dev liblzma-dev libssl-dev xz-utils\nzlib1g-dev", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-06-29 14:50:02 UTC", "RemoteUrl": "https://github.com/cran/oncoPredict", "RemoteRef": "HEAD", "RemoteSha": "a7646429fde113dd096f372626f2f0c116ba22fc", "MD5sum": "d8c775b9b2937b7f057f2aa2673f42b4", "_user": "cran", "_type": "src", "_file": "oncoPredict_1.3.1.tar.gz", "_fileid": "e86998c67a48adfe5a6b320b8c6fa972bbb4943c33e43635b188032e9a15b69d", "_filesize": 2619636, "_sha256": "e86998c67a48adfe5a6b320b8c6fa972bbb4943c33e43635b188032e9a15b69d", "_created": "2026-06-29T20:02:11.000Z", "_published": "2026-06-29T20:10:29.881Z", "_distro": "resolute", "_jobs": [ { "job": 84145668110, "time": 429, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7963228575" }, { "job": 84145668106, "time": 430, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "7963229452" }, { "job": 84144412129, "time": 389, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "7963066931" }, { "job": 84145668152, "time": 261, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7963165974" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/28398778367", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/oncoPredict", "_commit": { "id": "a7646429fde113dd096f372626f2f0c116ba22fc", "author": "Robert Gruener ", "committer": "cran-robot ", "message": "version 1.3.1\n", "time": 1782744602 }, "_maintainer": { "name": "Robert Gruener", "email": "rgruener@umn.edu", "login": "rfgruener", "description": "Post-Doctoral Fellow at the University of Minnesota in the lab of Stephanie Huang. ", "uuid": 32221440, "orcid": "0000-0002-8166-2772" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "parallel", "role": "Imports" }, { "package": "ridge", "role": "Imports" }, { "package": "car", "role": "Imports" }, { "package": "glmnet", "role": "Imports" }, { "package": "pls", "role": "Imports" }, { "package": "sva", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "GenomicFeatures", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "TxDb.Hsapiens.UCSC.hg19.knownGene", "role": "Suggests" }, { "package": "TCGAbiolinks", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-27", "n": 1 } ], "_tags": [ { "name": "1.3.1", "date": "2026-06-29" } ], "_topics": [ "sva", "limma", "stringr", "biomart", "genefilter", "genomicfeatures", "tcgabiolinks", "biocgenerics", "genomicranges", "iranges", "s4vectors" ], "_stars": 0, "_contributors": [ { "user": "maese005", "count": 2, "uuid": 62571435 }, { "user": "rfgruener", "count": 2, "uuid": 32221440 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 614, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 76, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/oncoPredict" }, "_devurl": "https://github.com/huanglabumn/oncopredict", "_searchresults": 87, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/oncoPredict.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_releases": [ { "version": "0.1", "date": "2021-06-04" }, { "version": "0.2", "date": "2021-09-24" }, { "version": "1.2", "date": "2024-04-05" }, { "version": "1.3.1", "date": "2026-06-29" } ], "_exports": [ "calcPhenotype", "completeMatrix", "doVariableSelection", "glds", "homogenizeData", "idwas", "map_cnv", "predictionAccuracybyCV", "summarizeGenesByMean" ], "_help": [ { "page": "calcPhenotype", "title": "Generate predicted drug sensitivity scores", "topics": [ "calcPhenotype" ] }, { "page": "completeMatrix", "title": "This function performs an iterative matrix completion algorithm to predict drug response for pre-clinical data when there are missing ('NA') values.", "topics": [ "completeMatrix" ] }, { "page": "doVariableSelection", "title": "Remove genes with low variation.", "topics": [ "doVariableSelection" ] }, { "page": "glds", "title": "This function determines drug-gene associations for pre-clinical data.", "topics": [ "glds" ] }, { "page": "homogenizeData", "title": "Homogenizes two expression matrices", "topics": [ "homogenizeData" ] }, { "page": "idwas", "title": "This function will test every drug against CNA amplifications or somatic mutations for your cancer type.", "topics": [ "idwas" ] }, { "page": "map_cnv", "title": "This function maps cnv data to genes.", "topics": [ "map_cnv" ] }, { "page": "predictionAccuracybyCV", "title": "Calculate Cross-Validation Scores using OncoPredict", "topics": [ "predictionAccuracybyCV" ] }, { "page": "summarizeGenesByMean", "title": "Average over duplicate gene values", "topics": [ "summarizeGenesByMean" ] } ], "_readme": "https://github.com/cran/oncoPredict/raw/HEAD/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "backports", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "boot", "broom", "cachem", "car", "carData", "cigarillo", "cli", "codetools", "colorspace", "cowplot", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "Deriv", "doBy", "dplyr", "edgeR", "farver", "fastmap", "foreach", "forecast", "formatR", "Formula", "fracdiff", "futile.logger", "futile.options", "genefilter", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glmnet", "glue", "gtable", "httr", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "lme4", "lmtest", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "memoise", "mgcv", "microbenchmark", "mime", "minqa", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "openssl", "pbkrtest", "pillar", "pkgconfig", "pls", "png", "purrr", "quantreg", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "Rdpack", "reformulas", "restfulr", "Rhtslib", "ridge", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "shape", "snow", "SparseArray", "SparseM", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sva", "sys", "tibble", "tidyr", "tidyselect", "timeDate", "urca", "utf8", "vctrs", "viridisLite", "withr", "XML", "xtable", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "calcPhenotype.Rmd", "filename": "calcPhenotype.html", "title": "calcPhenotype", "engine": "knitr::rmarkdown", "headings": [], "created": "2021-06-04 05:20:05", "modified": "2026-06-29 14:50:02", "commits": 4 }, { "source": "cnv.Rmd", "filename": "cnv.html", "title": "cnv", "engine": "knitr::rmarkdown", "headings": [], "created": "2021-06-04 05:20:05", "modified": "2026-06-29 14:50:02", "commits": 4 }, { "source": "glds.Rmd", "filename": "glds.html", "title": "glds", "engine": "knitr::rmarkdown", "headings": [], "created": "2021-06-04 05:20:05", "modified": "2026-06-29 14:50:02", "commits": 4 }, { "source": "mut.Rmd", "filename": "mut.html", "title": "mut", "engine": "knitr::rmarkdown", "headings": [], "created": "2021-06-04 05:20:05", "modified": "2026-06-29 14:50:02", "commits": 4 } ], "_score": 4.2405492482825995, "_indexed": true, "_nocasepkg": "oncopredict", "_universes": [ "cran", "rfgruener", "huanglabumn" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.1", "date": "2026-06-29T20:06:37.000Z", "distro": "resolute", "commit": "a7646429fde113dd096f372626f2f0c116ba22fc", "fileid": "cd89e4c674e006759f3c1659e8511330e8a5670db6be784ae539f37b09c87c1e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/28398778367" }, { "r": "4.6.1", "os": "linux", "version": "1.3.1", "date": "2026-06-29T20:06:34.000Z", "distro": "resolute", "commit": "a7646429fde113dd096f372626f2f0c116ba22fc", "fileid": "8f0a8d02eef794cf7513a4beed678453689b3998daea40320c48960e9843fa17", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/28398778367" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.1", "date": "2026-06-29T20:07:09.000Z", "commit": "a7646429fde113dd096f372626f2f0c116ba22fc", "fileid": "cdcc2e3d1d07a10652504e7087d302ea9c05eb741cc22b54280dac690ea0b0ba", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/28398778367" } ] }