{ "_id": "6ae71e351e2c7b3a4f52fc7b", "Package": "RPA", "Type": "Package", "Title": "RPA: Robust Probabilistic Averaging for probe-level analysis", "Encoding": "UTF-8", "Version": "1.69.0", "Date": "2023-04-07", "Authors@R": "person(given = \"Leo\",\nfamily = \"Lahti\",\nrole = c(\"aut\", \"cre\"),\nemail = \"leo.lahti@iki.fi\",\ncomment = c(ORCID = \"0000-0001-5537-637X\"))", "biocViews": "GeneExpression, Microarray, Preprocessing, QualityControl", "Description": "Probabilistic analysis of probe reliability and\ndifferential gene expression on short oligonucleotide arrays.", "License": "BSD_2_clause + file LICENSE", "URL": "https://github.com/antagomir/RPA", "BugReports": "https://github.com/antagomir/RPA", "VignetteBuilder": "knitr", "RoxygenNote": "7.2.3", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:34:04 UTC", "RemoteUrl": "https://github.com/bioc/RPA", "RemoteRef": "HEAD", "RemoteSha": "173cf6b19aaca831c8888116bc07aa649569b52f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-01 11:04:53 UTC", "User": "root" }, "Author": "Leo Lahti [aut, cre] (ORCID: )", "Maintainer": "Leo Lahti ", "_user": "bioc", "_type": "src", "_file": "RPA_1.69.0.tar.gz", "_fileid": "https://r2.ropensci.org/91aa25582edbf0a4deaa556ce67881b2fa348a486bd150850ac7e33b23d548a9", "_filesize": 227663, "_sha256": "91aa25582edbf0a4deaa556ce67881b2fa348a486bd150850ac7e33b23d548a9", "_expires": "2027-02-09T11:10:43.000Z", "_created": "2026-11-01T11:04:53.000Z", "_published": "2026-11-01T11:10:45.840Z", "_upstream": "https://github.com/bioc/RPA", "_status": "success", "_maintainer": { "name": "Leo Lahti", "email": "leo.lahti@iki.fi", "login": "antagomir", "bluesky": "@antagomir.bsky.social", "linkedin": "in/leo-lahti-b942ba3", "description": "Prof. in Data Science. Department of Computing, University of Turku, Finland. Complex natural and social systems.", "uuid": 1228382, "orcid": "0000-0001-5537-637X" }, "_jobs": [ { "job": 124829710623, "time": 161, "config": "bioc-checks", "r": "4.6.2", "check": "ERROR", "artifact": "13080729194" }, { "job": 124829710633, "time": 304, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13081570208" }, { "job": 124829710589, "time": 296, "config": "linux-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13081410532" }, { "job": 124829710642, "time": 197, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "13080669577" }, { "job": 124829710636, "time": 178, "config": "macos-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13080338994" }, { "job": 124828805088, "time": 245, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13080454733" }, { "job": 124829710582, "time": 124, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13081510449" }, { "job": 124829710647, "time": 171, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13081325512" }, { "job": 124829710607, "time": 174, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "13081400366" }, { "job": 124829710663, "time": 173, "config": "windows-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13081630127" } ], "_bioccheck": { "error": 1, "warning": 4, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41299979791", "_commit": { "id": "173cf6b19aaca831c8888116bc07aa649569b52f", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379644 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.1", "role": "Depends" }, { "package": "affy", "role": "Depends" }, { "package": "BiocGenerics", "role": "Depends" }, { "package": "BiocStyle", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "rmarkdown", "role": "Depends" }, { "package": "phyloseq", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "parallel", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.69.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.68.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "geneexpression", "microarray", "preprocessing", "qualitycontrol" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 481, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 659, "source": "https://www.bioconductor.org/packages/stats/bioc/RPA" }, "_mentions": 19, "_searchresults": 24, "_abi": { "exports": [ { "key": "RPA::rpa.list", "hash": "8f1a7989657e3e2b" } ], "imports": [] }, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/RPA.html", "LICENSE" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "calculate.rpa", "collect.hyperparameters", "d.update.fast", "estimate.affinities", "estimate.hyperparameters", "frpa", "get.probe.matrix", "get.probe.parameters", "get.probeset", "hyperparameter.update", "n.phylotypes.per.oligo", "online.quantile", "probe.parameters.tolist", "probe.performance", "probeplot", "probetable", "rpa", "rpa.complete", "rpa.fit", "RPA.iteration", "rpa.online", "rpa.plot", "RPA.preprocess", "rpa.summarize", "rpaplot", "sample.probeset", "summarize_probedata", "summarize.batch", "summarize.batches", "summarize.rpa", "summarize.sum", "updating.hyperparameters" ], "_help": [ { "page": "RPA-package", "title": "RPA: probabilistic analysis of probe reliability and gene expression", "topics": [ "RPA-package", "RPA" ] }, { "page": "calculate.rpa", "title": "RPA with HITChip", "topics": [ "calculate.rpa" ] }, { "page": "collect.hyperparameters", "title": "collect.hyperparameters", "topics": [ "collect.hyperparameters" ] }, { "page": "d.update.fast", "title": "Fast d update", "topics": [ "d.update.fast" ] }, { "page": "estimate.affinities", "title": "estimate.affinities", "topics": [ "estimate.affinities" ] }, { "page": "estimate.hyperparameters", "title": "estimate.hyperparameters", "topics": [ "estimate.hyperparameters" ] }, { "page": "frpa", "title": "frpa", "topics": [ "frpa" ] }, { "page": "get.batches", "title": "get.batches Split data into batches", "topics": [ "get.batches" ] }, { "page": "get.probe.matrix", "title": "get.probe.matrix", "topics": [ "get.probe.matrix" ] }, { "page": "get.probe.parameters", "title": "get.probe.parameters", "topics": [ "get.probe.parameters" ] }, { "page": "get.probeset", "title": "Get probeset", "topics": [ "get.probeset" ] }, { "page": "hyperparameter.update", "title": "hyperparameter.update", "topics": [ "hyperparameter.update" ] }, { "page": "n.phylotypes.per.oligo", "title": "n.phylotypes.per.oligo", "topics": [ "n.phylotypes.per.oligo" ] }, { "page": "online.quantile", "title": "online.quantile Quantile normalization tools for online preprocessing. Estimate quantiles for quantile normalization based on subset of the data (random, or specified by the user).", "topics": [ "online.quantile" ] }, { "page": "probe.parameters.tolist", "title": "probe.parameters.tolist", "topics": [ "probe.parameters.tolist" ] }, { "page": "probe.performance", "title": "Probe performance", "topics": [ "probe.performance" ] }, { "page": "probeplot", "title": "probeplot Plot RPA results and probe-level data for a specified probeset.", "topics": [ "probeplot" ] }, { "page": "probetable", "title": "probetable", "topics": [ "probetable" ] }, { "page": "rpa", "title": "rpa", "topics": [ "rpa" ] }, { "page": "rpa.complete", "title": "Complete RPA preprocessing", "topics": [ "rpa.complete" ] }, { "page": "rpa.fit", "title": "RPA fit", "topics": [ "rpa.fit" ] }, { "page": "RPA.iteration", "title": "RPA iteration", "topics": [ "RPA.iteration" ] }, { "page": "rpa.online", "title": "rpa.online", "topics": [ "rpa.online" ] }, { "page": "rpa.plot", "title": "rpa.plot", "topics": [ "rpa.plot" ] }, { "page": "RPA.preprocess", "title": "RPA preprocessing", "topics": [ "RPA.preprocess" ] }, { "page": "rpa.summarize", "title": "rpa.summarize", "topics": [ "rpa.summarize" ] }, { "page": "rpaplot", "title": "rpaplot Plot RPA results and probe-level data for a specified probeset.", "topics": [ "rpaplot" ] }, { "page": "sample.probeset", "title": "sample.probeset", "topics": [ "sample.probeset" ] }, { "page": "summarize_probedata", "title": "Summarize probedata", "topics": [ "summarize_probedata" ] }, { "page": "summarize.batch", "title": "summarize.batch", "topics": [ "summarize.batch" ] }, { "page": "summarize.batches", "title": "summarize.batches", "topics": [ "summarize.batches" ] }, { "page": "summarize.rpa", "title": "RPA summarization", "topics": [ "summarize.rpa" ] }, { "page": "summarize.sum", "title": "Sum-based probe summarization", "topics": [ "summarize.sum" ] }, { "page": "updating.hyperparameters", "title": "updating hyperparameters", "topics": [ "updating.hyperparameters" ] } ], "_readme": "https://github.com/bioc/RPA/raw/HEAD/README.md", "_rundeps": [ "ade4", "affy", "affyio", "ape", "base64enc", "Biobase", "BiocGenerics", "BiocManager", "BiocStyle", "biomformat", "Biostrings", "bookdown", "bslib", "cachem", "cli", "cluster", "codetools", "cpp11", "crayon", "data.table", "digest", "evaluate", "farver", "fastmap", "fontawesome", "foreach", "fs", "generics", "ggplot2", "glue", "gtable", "highr", "htmltools", "igraph", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "memoise", "mgcv", "mime", "multtest", "nlme", "permute", "phyloseq", "pixmap", "pkgconfig", "plyr", "preprocessCore", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape2", "rlang", "rmarkdown", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "sp", "stringi", "stringr", "survival", "tinytex", "vctrs", "vegan", "viridisLite", "withr", "xfun", "XVector", "yaml" ], "_vignettes": [ { "source": "RPA.Rmd", "filename": "RPA.html", "title": "Robust Probabilistic Averaging (RPA)", "author": "Leo Lahti", "engine": "knitr::rmarkdown", "headings": [ "Robust Probabilistic Averaging (RPA)", "How to use", "Citing RPA" ], "created": "2014-06-10 18:39:49", "modified": "2022-09-29 17:07:45", "commits": 5 } ], "_score": 5.857332496431269, "_indexed": true, "_nocasepkg": "rpa", "_universes": [ "bioc", "antagomir" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.69.0", "date": "2026-11-01T11:08:31.000Z", "distro": "resolute", "commit": "173cf6b19aaca831c8888116bc07aa649569b52f", "fileid": "https://r2.ropensci.org/65464c21f8854aa263bfef1789741bf917372b3a6b0c0880996d42ad1d0d6485", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41299979791" }, { "r": "4.6.2", "os": "linux", "version": "1.69.0", "date": "2026-11-01T11:08:30.000Z", "distro": "resolute", "commit": "173cf6b19aaca831c8888116bc07aa649569b52f", "fileid": "https://r2.ropensci.org/39ebcfb1d111315dd0e3d22c9859eef2fd7684e0e578ae442ad403ee88277986", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41299979791" }, { "r": "4.5.3", "os": "mac", "version": "1.69.0", "date": "2026-11-01T11:07:05.000Z", "commit": "173cf6b19aaca831c8888116bc07aa649569b52f", "fileid": "https://r2.ropensci.org/21e2fd523ac93be92ac4bd3784f2571031985fb02ad5ab4b02ff9162299d80ae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41299979791" }, { "r": "4.6.2", "os": "mac", "version": "1.69.0", "date": "2026-11-01T11:06:52.000Z", "commit": "173cf6b19aaca831c8888116bc07aa649569b52f", "fileid": "https://r2.ropensci.org/3f55470f1893d4c85165efc84b3aa89039e696a4915627619688a66400407c2a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41299979791" }, { "r": "4.6.0", "os": "wasm", "version": "1.69.0", "date": "2026-11-01T11:07:23.000Z", "commit": "173cf6b19aaca831c8888116bc07aa649569b52f", "fileid": "https://r2.ropensci.org/c05189b98cb52fa2426d1499743a1fd6a018518841b0134146df02a3d4dc0d90", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41299979791" }, { "r": "4.7.0", "os": "win", "version": "1.69.0", "date": "2026-11-01T11:06:17.000Z", "commit": "173cf6b19aaca831c8888116bc07aa649569b52f", "fileid": "https://r2.ropensci.org/3cfec159925ef5ef725f878677f1ffb33a3c39b15ad5adc799cd77014ab1863a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41299979791" }, { "r": "4.5.3", "os": "win", "version": "1.69.0", "date": "2026-11-01T11:06:26.000Z", "commit": "173cf6b19aaca831c8888116bc07aa649569b52f", "fileid": "https://r2.ropensci.org/c3bcaddb7a1e11403edef59f1abc660592fbaae890161a2d38a7039923f43d90", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41299979791" }, { "r": "4.6.2", "os": "win", "version": "1.69.0", "date": "2026-11-01T11:06:23.000Z", "commit": "173cf6b19aaca831c8888116bc07aa649569b52f", "fileid": "https://r2.ropensci.org/eb3b839cd4cb7f8929dc503e12510f8a7a88e3145b0aac504e4080bfeb450871", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41299979791" } ] }