{ "_id": "6a1bce9c1d7bb097a0a13ee6", "Package": "plasma", "Title": "Partial LeAst Squares for Multiomic Analysis", "Version": "1.1.5", "Date": "2025-05-08", "Authors@R": "c(person(\"Kevin R.\", \"Coombes\", role = c(\"cre\", \"aut\"),\nemail = \"krc@silicovore.com\"),\nperson(\"Kyoko\", \"Yamaguchi\", role = \"aut\"),\nperson(\"Salma\", \"Abdelbaky\", role = \"aut\"))", "Description": "Contains tools for supervised analyses of incomplete,\noverlapping multiomics datasets. Applies partial least squares\nin multiple steps to find models that predict survival\noutcomes. See Yamaguchi et al. (2023)\n.", "License": "Apache License (== 2.0)", "LazyLoad": "yes", "URL": "http://oompa.r-forge.r-project.org/", "VignetteBuilder": "R.rsp", "Config/pak/sysreqs": "cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev\nmake texlive libicu-dev libpng-dev libuv1-dev libxml2-dev\nlibgl1-mesa-dev zlib1g-dev", "Repository": "https://r-forge.r-universe.dev", "Date/Publication": "2026-05-22 18:40:06 UTC", "RemoteUrl": "https://github.com/r-forge/oompa", "RemoteRef": "HEAD", "RemoteSha": "969e77c65694e77068421e66612b9fc687a5a023", "RemoteSubdir": "pkg/plasma", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 19:40:15 UTC", "User": "root" }, "Author": "Kevin R. Coombes [cre, aut],\nKyoko Yamaguchi [aut],\nSalma Abdelbaky [aut]", "Maintainer": "Kevin R. Coombes ", "MD5sum": "a7041a2bb85451cb91d7acc858c6189d", "_user": "r-forge", "_type": "src", "_file": "plasma_1.1.5.tar.gz", "_fileid": "f20a6f29d1a5b48f0734c43eda63ea808e65891d15b124a6c883fbe7f72456fd", "_filesize": 2031356, "_sha256": "f20a6f29d1a5b48f0734c43eda63ea808e65891d15b124a6c883fbe7f72456fd", "_created": "2026-05-29T19:40:15.000Z", "_published": "2026-05-31T06:01:00.908Z", "_distro": "noble", "_jobs": [ { "job": 78703879423, "time": 208, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "FAIL", "artifact": "" }, { "job": 78703879412, "time": 215, "config": "linux-release-x86_64", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 78703879414, "time": 85, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 78703879424, "time": 98, "config": "macos-release-arm64", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 78703879393, "time": 324, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7299520627" }, { "job": 78703879415, "time": 216, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 78703879431, "time": 100, "config": "windows-devel", "r": "4.7.0", "check": "FAIL", "artifact": "" }, { "job": 78703879428, "time": 137, "config": "windows-oldrel", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 78703879421, "time": 84, "config": "windows-release", "r": "4.6.0", "check": "FAIL", "artifact": "" } ], "_buildurl": "https://github.com/r-universe/r-forge/actions/runs/26658081106", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/r-forge/oompa", "_commit": { "id": "969e77c65694e77068421e66612b9fc687a5a023", "author": "krcoombes (Kevin Coombes) ", "committer": "krcoombes (Kevin Coombes) ", "message": "Added XKCD color names.\n\ngit-svn-id: svn://svn.r-forge.r-project.org/svnroot/oompa@707 edb9625f-4e0d-4859-8d74-9fd3b1da38cb\n", "time": 1779475206 }, "_maintainer": { "name": "Kevin R. Coombes", "email": "krc@silicovore.com" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "pls", "role": "Imports" }, { "package": "plsRcox", "role": "Imports" }, { "package": "Polychrome", "version": ">= 1.5.0", "role": "Imports" }, { "package": "viridisLite", "role": "Imports" }, { "package": "beanplot", "role": "Imports" }, { "package": "oompaBase", "role": "Imports" }, { "package": "R.rsp", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "ClassDiscovery", "role": "Suggests" } ], "_owner": "r-forge", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-22", "n": 2 }, { "week": "2025-36", "n": 1 }, { "week": "2025-40", "n": 1 }, { "week": "2025-45", "n": 2 }, { "week": "2025-46", "n": 1 }, { "week": "2025-47", "n": 2 }, { "week": "2026-02", "n": 1 }, { "week": "2026-18", "n": 8 }, { "week": "2026-19", "n": 6 }, { "week": "2026-21", "n": 1 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "krcoombes", "count": 582, "uuid": 5930440 }, { "user": "lmsstudios", "count": 101, "uuid": 97995137 }, { "user": "yamachan18", "count": 19, "uuid": 81639585 }, { "user": "theussl", "count": 1, "uuid": 22165873 } ], "_userbio": { "uuid": 75573726, "type": "organization", "name": " R-Forge", "description": "git-svn mirrors from R-Forge" }, "_downloads": { "count": 600, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/plasma" }, "_devurl": "https://github.com/r-forge/oompa", "_searchresults": 16, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/plasma.html", "manual.pdf" ], "_homeurl": "https://github.com/r-forge/oompa", "_realowner": "r-forge", "_cranurl": true, "_releases": [ { "version": "0.9.21", "date": "2022-12-06" }, { "version": "1.0.0", "date": "2023-03-13" }, { "version": "1.1.3", "date": "2024-04-28" }, { "version": "1.1.4", "date": "2025-04-07" }, { "version": "1.1.5", "date": "2025-05-27" } ], "_exports": [ "barplot", "combineAllWeights", "fitCoxModels", "fitSingleModel", "getAllWeights", "getCompositeWeights", "getFinalWeights", "getSizes", "getTop", "heat", "image", "interpret", "loadESCAdata", "loadLUSCdata", "meanModeImputer", "pickSignificant", "plasma", "plasmaEnv", "plot", "predict", "prepareMultiOmics", "samplingImputer", "stdize", "summary" ], "_datasets": [ { "name": "mirESCA", "title": "ESCA type data", "object": "mirESCA", "file": "mirESCA.rda", "class": [ "data.frame" ], "fields": [ "ID", "Type" ], "rows": 195, "table": true, "tojson": true }, { "name": "tfESCA", "title": "ESCA type data", "object": "tfESCA", "file": "tfESCA.rda", "class": [ "data.frame" ], "fields": [ "ID", "Type" ], "rows": 196, "table": true, "tojson": true } ], "_help": [ { "page": "06-CombinedWeights-class", "title": "Class '\"CombinedWeights\"'", "topics": [ "combineAllWeights", "CombinedWeights", "CombinedWeights-class", "image,CombinedWeights-method", "interpret", "stdize", "summary,CombinedWeights-method" ] }, { "page": "05-Contribution-class", "title": "Class '\"Contribution\"'", "topics": [ "Contribution", "Contribution-class", "getAllWeights", "getCompositeWeights", "getFinalWeights", "getTop", "heat", "heat,Contribution-method", "image,Contribution-method", "pickSignificant", "summary,Contribution-method", "[,Contribution,ANY,ANY,ANY-method" ] }, { "page": "07-esca-type-data", "title": "ESCA type data", "topics": [ "mirESCA", "tfESCA" ] }, { "page": "00-imputation", "title": "Imputation", "topics": [ "meanModeImputer", "samplingImputer" ] }, { "page": "01-MultiOmics", "title": "Class '\"MultiOmics\"'", "topics": [ "MultiOmics", "MultiOmics-class", "plot,MultiOmics,missing-method", "prepareMultiOmics", "summary,MultiOmics-method", "validMultiOmics", "[,MultiOmics,ANY,ANY,ANY-method" ] }, { "page": "03-manyCoxModels", "title": "Class '\"MultiplePLSCoxModels\"'", "topics": [ "fitCoxModels", "getSizes", "MultiplePLSCoxModels", "MultiplePLSCoxModels-class", "plot,MultiplePLSCoxModels,missing-method", "predict,MultiplePLSCoxModels-method", "summary,MultiplePLSCoxModels-method", "validMultipleCoxModels", "[,MultiplePLSCoxModels,ANY,ANY,ANY-method" ] }, { "page": "04-plasma-class", "title": "Class '\"plasma\"'", "topics": [ "barplot,plasma-method", "plasma", "plasma-class", "plot,plasma,missing-method", "predict,plasma-method", "summary,plasma-method" ] }, { "page": "04-plasmaPredictions-class", "title": "Class '\"plasmaPredictions\"'", "topics": [ "plasmaPredictions", "plasmaPredictions-class", "plot,plasmaPredictions,missing-method" ] }, { "page": "02-fitCoxModel", "title": "Class '\"SingleModel\"'", "topics": [ "fitSingleModel", "plot,SingleModel,missing-method", "predict,SingleModel-method", "SingleModel-class", "summary,SingleModel-method" ] }, { "page": "01-TCGA-ESCA-data", "title": "Esophageal carcinoma (ESCA) data or lung squamous cell carcinoma (LUSC) data from The Cancer Genome Atlas (TCGA).", "topics": [ "assemble", "loadESCAdata", "loadLUSCdata", "m450info", "Outcome", "plasmaEnv", "TCGA-ESCA", "TCGA-LUSC" ] } ], "_rundeps": [ "abind", "backports", "base64enc", "beanplot", "BH", "BiocParallel", "bipartite", "boot", "bootstrap", "broom", "bslib", "cachem", "car", "carData", "checkmate", "class", "cli", "cluster", "coda", "codetools", "colorspace", "corpcor", "cowplot", "cpp11", "data.table", "Deriv", "diagram", "digest", "doBy", "dotCall64", "dplyr", "ellipse", "evaluate", "farver", "fastmap", "fields", "fontawesome", "forecast", "foreign", "formatR", "Formula", "fracdiff", "fs", "futile.logger", "futile.options", "future", "future.apply", "generics", "ggplot2", "ggrepel", "globals", "glue", "gridExtra", "gtable", "highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "igraph", "ipred", "isoband", "jquerylib", "jsonlite", "kernlab", "KernSmooth", "knitr", "labeling", "lambda.r", "lars", "lattice", "lava", "lifecycle", "listenv", "lme4", "lmtest", "magrittr", "maps", "MASS", "Matrix", "MatrixModels", "matrixStats", "memoise", "mgcv", "microbenchmark", "mime", "minqa", "mixOmics", "modelr", "multcomp", "mvtnorm", "network", "nlme", "nloptr", "nnet", "numDeriv", "oompaBase", "parallelly", "pbkrtest", "permute", "pillar", "pkgconfig", "pls", "plsRcox", "plsRglm", "plyr", "polspline", "Polychrome", "prodlim", "progressr", "purrr", "quantreg", "R6", "rappdirs", "rARPACK", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "reshape2", "rgl", "risksetROC", "rlang", "rmarkdown", "rmeta", "rms", "rpart", "RSpectra", "rstudioapi", "S7", "sandwich", "sass", "scales", "scatterplot3d", "shape", "sna", "snow", "spam", "SparseM", "SQUAREM", "statnet.common", "stringi", "stringr", "SuppDists", "survAUC", "survcomp", "survival", "survivalROC", "TH.data", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "urca", "utf8", "vctrs", "vegan", "viridisLite", "withr", "xfun", "yaml", "zoo" ], "_vignettes": [ { "source": "interpret.pdf.asis", "filename": "interpret.pdf", "title": "plasma: Interpretation", "engine": "R.rsp::asis", "headings": [], "created": "2022-10-25 14:44:28", "modified": "2022-10-25 14:44:28", "commits": 1 }, { "source": "plasma.pdf.asis", "filename": "plasma.pdf", "title": "plasma: Partial LeAst Squares for Multiomics Analysis", "engine": "R.rsp::asis", "headings": [], "created": "2022-10-25 14:44:28", "modified": "2022-12-01 22:10:51", "commits": 2 } ], "_score": 4.982271233039569, "_indexed": true, "_nocasepkg": "plasma", "_universes": [ "r-forge" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.5", "date": "2026-05-04T21:16:29.000Z", "distro": "noble", "commit": "71346dde134d0cfb746e0b5891b53261b651f2f2", "fileid": "0233eeca6404d4a9be020d2a4d8551ddb4b42bc8fa7b5ac9556916e1c5a68234", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/r-forge/actions/runs/25343594923" }, { "r": "4.5.3", "os": "mac", "version": "1.1.5", "date": "2026-05-04T21:14:44.000Z", "commit": "71346dde134d0cfb746e0b5891b53261b651f2f2", "fileid": "b6e2f4dd7aaf2ccfeef23a25712d71a469a60e900389a2fd34ede6606ceaf41c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/r-forge/actions/runs/25343594923" }, { "r": "4.6.0", "os": "mac", "version": "1.1.5", "date": "2026-05-04T21:14:51.000Z", "commit": "71346dde134d0cfb746e0b5891b53261b651f2f2", "fileid": "fae0d4ef032d670843f90413f3f2fa0f6552b2899ebd5bd37a1bc7c208ef8488", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/r-forge/actions/runs/25343594923" }, { "r": "4.7.0", "os": "win", "version": "1.1.5", "date": "2026-05-04T21:16:02.000Z", "commit": "71346dde134d0cfb746e0b5891b53261b651f2f2", "fileid": "f8bb9d2b09284b8bd28d67ccf809446925813b7e593e3b6e6c2d35091cc3f4f2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/r-forge/actions/runs/25343594923" }, { "r": "4.5.3", "os": "win", "version": "1.1.5", "date": "2026-05-04T21:14:31.000Z", "commit": "71346dde134d0cfb746e0b5891b53261b651f2f2", "fileid": "2d629a60979103aaefe0e2c3f837a07b2f1f99ba455403cc609ce52747360787", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/r-forge/actions/runs/25343594923" }, { "r": "4.6.0", "os": "win", "version": "1.1.5", "date": "2026-05-04T21:20:50.000Z", "commit": "71346dde134d0cfb746e0b5891b53261b651f2f2", "fileid": "0c0b1c333724841ddbb34f6f98a2fdaa1b660758a85f517e7854aaae1eb42b40", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/r-forge/actions/runs/25343594923" }, { "r": "4.5.1", "os": "wasm", "version": "1.1.5", "date": "2026-05-08T15:33:03.000Z", "commit": "bc19904c85a0e78c0c172c97aba1f8c30f1be0f3", "fileid": "703ced1e6de15b80b8d619e3208b697411cb023ce7cc2175f2bc69cf08549fc0", "status": "success", "buildurl": "https://github.com/r-universe/r-forge/actions/runs/25563805983" }, { "r": "4.6.0", "os": "linux", "version": "1.1.5", "date": "2026-05-29T19:40:16.000Z", "distro": "noble", "commit": "969e77c65694e77068421e66612b9fc687a5a023", "fileid": "4b4d68d3e6d4d2bf265d2b67677fee9c79b9556262fab1a2b0c35c60f3e5fb45", "status": "success", "buildurl": "https://github.com/r-universe/r-forge/actions/runs/26658081106" } ] }