{
"_id": "6a2723e624555f66ed529734",
"Type": "Package",
"Package": "OlinkAnalyzeVignettes",
"Title": "Vignettes for Analyzing Data using 'OlinkAnalyze'",
"Version": "1.0.1",
"Authors@R": "c(\nperson(\"Kathleen\", \"Nevola\", , \"biostattools@olink.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-5183-6444\", \"kathy-nevola\")),\nperson(\"Marianne\", \"Sandin\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-6186-963X\", \"marisand\")),\nperson(\"Jamey\", \"Guess\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-4017-0923\", \"jrguess\")),\nperson(\"Simon\", \"Forsberg\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-7451-9222\", \"simfor\")),\nperson(\"Christoffer\", \"Cambronero\", role = \"aut\",\ncomment = c(\"Orbmac\")),\nperson(\"Pascal\", \"Pucholt\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-3342-1373\", \"AskPascal\")),\nperson(\"Boxi\", \"Zhang\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-7758-6204\", \"boxizhang\")),\nperson(\"Masoumeh\", \"Sheikhi\", role = \"aut\",\ncomment = c(\"MasoumehSheikhi\")),\nperson(\"Klev\", \"Diamanti\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-4922-8415\", \"klevdiamanti\")),\nperson(\"Amrita\", \"Kar\", role = \"aut\",\ncomment = c(\"amrita-kar\")),\nperson(\"Lei\", \"Conze\", role = \"aut\",\ncomment = c(\"leiliuC\")),\nperson(\"Kristyn\", \"Chin\", role = \"aut\",\ncomment = c(\"kristynchin-olink\")),\nperson(\"Danai\", \"Topouza\", role = \"aut\",\ncomment = c(\"dtopouza\", ORCID = \"0000-0002-6897-9281\")),\nperson(\"Stephen\", \"Pollo\", role = \"aut\",\ncomment = c(\"spollo-olprot\", ORCID = \"0000-0001-9252-4976\")),\nperson(\"Kang\", \"Dong\", role = \"aut\",\ncomment = c(\"KangD-dev\", ORCID = \"0000-0002-4567-5007\")),\nperson(\"Kristian\", \"Hodén\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-0354-0662\", \"kristianHoden\")),\nperson(\"Per\", \"Eriksson\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-7633-403X\", \"b_watcher\")),\nperson(\"Nicola\", \"Moloney\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-4967-3284\")),\nperson(\"Britta\", \"Lötstedt\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-3545-5489\")),\nperson(\"Emmett\", \"Sprecher\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-7710-695X\")),\nperson(\"Jessica\", \"Barbagallo\", role = \"ctb\",\ncomment = c(\"jbarbagallo\")),\nperson(\"Olof\", \"Mansson\", role = \"ctr\",\ncomment = c(\"olofmansson\")),\nperson(\"Ola\", \"Caster\", role = \"ctb\",\ncomment = c(\"OlaCaster\")),\nperson(\"Olink\", role = c(\"cph\", \"fnd\"))\n)",
"Description": "Exemplifying analysis of large-scale protein data from the\n'Olink platform', primarily relative protein expression data\nthat has been exported from 'Olink NPX Software', as well as\nQUANT data from 'Olink'. QUANT data is log-transformed.\nMaterials focus on reading data, demonstrating data wrangling\nand quality control analysis, performing statistical analysis\nand generating figures to visualize the results of the\nstatistical analysis. The goal of this package is to guide\nusers extract biological insights from large-scale protein data\nrun on the 'Olink platform'. More information on 'Olink' data\ncan be found at .",
"Contact": "biostattools@olink.com",
"URL": "https://olink.com/\nhttps://github.com/Olink-Proteomics/OlinkRPackage",
"License": "AGPL (>= 3)",
"Encoding": "UTF-8",
"VignetteBuilder": "knitr",
"Config/roxygen2/version": "8.0.0",
"NeedsCompilation": "no",
"Packaged": {
"Date": "2026-06-08 20:17:02 UTC",
"User": "root"
},
"Author": "Kathleen Nevola [aut, cre] (ORCID:\n, kathy-nevola),\nMarianne Sandin [aut] (ORCID:\n, marisand), Jamey Guess\n[aut] (ORCID: ,\njrguess), Simon Forsberg [aut] (ORCID:\n, simfor), Christoffer\nCambronero [aut] (Orbmac), Pascal Pucholt [aut] (ORCID:\n, AskPascal), Boxi Zhang\n[aut] (ORCID: ,\nboxizhang), Masoumeh Sheikhi [aut] (MasoumehSheikhi), Klev\nDiamanti [aut] (ORCID: ,\nklevdiamanti), Amrita Kar [aut] (amrita-kar), Lei Conze [aut]\n(leiliuC), Kristyn Chin [aut] (kristynchin-olink), Danai\nTopouza [aut] (dtopouza, ORCID:\n), Stephen Pollo [aut]\n(spollo-olprot, ORCID:\n), Kang Dong [aut]\n(KangD-dev, ORCID: ),\nKristian Hodén [ctb] (ORCID:\n, kristianHoden), Per\nEriksson [ctb] (ORCID: ,\nb_watcher), Nicola Moloney [ctb] (ORCID:\n), Britta Lötstedt [ctb]\n(ORCID: ), Emmett\nSprecher [ctb] (ORCID:\n), Jessica Barbagallo\n[ctb] (jbarbagallo), Olof Mansson [ctr] (olofmansson), Ola\nCaster [ctb] (OlaCaster), Olink [cph, fnd]",
"Maintainer": "Kathleen Nevola ",
"Repository": "https://cran.r-universe.dev",
"Date/Publication": "2026-06-08 16:32:12 UTC",
"RemoteUrl": "https://github.com/cran/OlinkAnalyzeVignettes",
"RemoteRef": "HEAD",
"RemoteSha": "c185521bb1030edb6b258dd72d0f168dd0c57c85",
"MD5sum": "49717689552323f50aa69fd87dfd4251",
"_user": "cran",
"_type": "src",
"_file": "OlinkAnalyzeVignettes_1.0.1.tar.gz",
"_fileid": "c501a288c4c608da6040a4603c4f91644c40111c3844f1041959bc32ecab5256",
"_filesize": 2099361,
"_sha256": "c501a288c4c608da6040a4603c4f91644c40111c3844f1041959bc32ecab5256",
"_created": "2026-06-08T20:17:02.000Z",
"_published": "2026-06-08T20:19:50.175Z",
"_distro": "noble",
"_jobs": [
{
"job": 80187580859,
"time": 133,
"config": "linux-devel-x86_64",
"r": "4.7.0",
"check": "OK",
"artifact": "7491415924"
},
{
"job": 80187580804,
"time": 135,
"config": "linux-release-x86_64",
"r": "4.6.0",
"check": "OK",
"artifact": "7491416020"
},
{
"job": 80186957947,
"time": 199,
"config": "source",
"r": "4.6.0",
"check": "OK",
"artifact": "7491367091"
},
{
"job": 80187580822,
"time": 127,
"config": "wasm-release",
"r": "4.6.0",
"check": "OK",
"artifact": "7491412959"
}
],
"_buildurl": "https://github.com/r-universe/cran/actions/runs/27164152751",
"_status": "success",
"_host": "GitHub-Actions",
"_upstream": "https://github.com/cran/OlinkAnalyzeVignettes",
"_commit": {
"id": "c185521bb1030edb6b258dd72d0f168dd0c57c85",
"author": "Kathleen Nevola ",
"committer": "cran-robot ",
"message": "version 1.0.1\n",
"time": 1780936332
},
"_maintainer": {
"name": "Kathleen Nevola",
"email": "biostattools@olink.com",
"login": "kathy-nevola",
"description": "",
"uuid": 72228735,
"orcid": "0000-0002-5183-6444"
},
"_registered": true,
"_dependencies": [
{
"package": "R",
"version": ">= 4.1.0",
"role": "Depends"
},
{
"package": "dplyr",
"version": ">= 1.2.0",
"role": "Suggests"
},
{
"package": "ggplot2",
"role": "Suggests"
},
{
"package": "ggpubr",
"role": "Suggests"
},
{
"package": "ggrepel",
"role": "Suggests"
},
{
"package": "kableExtra",
"role": "Suggests"
},
{
"package": "knitr",
"role": "Suggests"
},
{
"package": "OlinkAnalyze",
"role": "Suggests"
},
{
"package": "stringr",
"role": "Suggests"
},
{
"package": "tidyr",
"role": "Suggests"
}
],
"_owner": "cran",
"_selfowned": false,
"_usedby": 0,
"_updates": [
{
"week": "2026-24",
"n": 1
}
],
"_tags": [
{
"name": "1.0.1",
"date": "2026-06-08"
}
],
"_stars": 0,
"_contributors": [
{
"user": "kathy-nevola",
"count": 1,
"uuid": 72228735
}
],
"_userbio": {
"uuid": 6899542,
"type": "organization",
"name": "cran",
"description": "Unofficial read-only mirror of all CRAN R packages"
},
"_downloads": {
"count": 0,
"source": "https://cranlogs.r-pkg.org/downloads/total/last-month/OlinkAnalyzeVignettes"
},
"_devurl": "https://github.com/olink-proteomics/olinkrpackage",
"_searchresults": 0,
"_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/OlinkAnalyzeVignettes.html",
"manual.pdf"
],
"_cranurl": false,
"_releases": [
{
"version": "1.0.1",
"date": "2026-06-08"
}
],
"_exports": [
"open_docs"
],
"_help": [
{
"page": "open_docs",
"title": "Open the Olink Analyze GitHub repo page",
"topics": [
"open_docs"
]
}
],
"_rundeps": [],
"_vignettes": [
{
"source": "bridging_cross-product.Rmd",
"filename": "bridging_cross-product.html",
"title": "Bridging across NGS-based Olink^®^ products",
"engine": "knitr::rmarkdown",
"headings": [
"Introduction",
"Important Terminology",
"Within- and between-product bridging",
"Considerations for between-product bridging",
"Bridge Sample Selection",
"Workflow Overview",
"Import NPX files",
"Checking input datasets and bridging samples",
"Normalization",
"Determining bridging recommendations",
"Normalization using the median of paired differences",
"Quantile smoothing",
"Function Output",
"Evaluating the quality of bridging",
"Exporting Normalized Data",
"FAQs",
"Overlapping Assays within products",
"Downstream Analysis",
"Contact Us",
"Legal Disclaimer"
],
"created": "2026-06-08 16:32:12",
"modified": "2026-06-08 16:32:12",
"commits": 1
},
{
"source": "lod.Rmd",
"filename": "lod.html",
"title": "Calculating LOD from Olink® Explore data",
"engine": "knitr::rmarkdown",
"headings": [
"Introduction",
"Integrating LOD",
"Import Olink NGS datasets",
"A note on calculating LOD with clean_npx()",
"Integrating Negative Control LOD",
"A note on calculating LOD from counts",
"Integrating Fixed LOD",
"When to Use Fixed LOD vs NC LOD",
"Integrating Both NC LOD and Fixed LOD",
"Adjusting LOD for Intensity Normalized Data",
"Handling LOD in Bridge-Normalized Data",
"Export Olink NGS Data with LOD",
"Contact Us",
"Legal Disclaimer"
],
"created": "2026-06-08 16:32:12",
"modified": "2026-06-08 16:32:12",
"commits": 1
},
{
"source": "bridging_introduction.Rmd",
"filename": "bridging_introduction.html",
"title": "Introduction to bridging Olink® NPX datasets",
"engine": "knitr::rmarkdown",
"headings": [
"Selecting bridge samples",
"Setup bridging datasets",
"Check bridging datasets",
"Bridging between two data sets",
"Perform bridging with non-matching sample names",
"Bridging evaluation",
"Export Bridged data",
"Contact Us",
"Legal Disclaimer"
],
"created": "2026-06-08 16:32:12",
"modified": "2026-06-08 16:32:12",
"commits": 1
},
{
"source": "outlier_exclusion.Rmd",
"filename": "outlier_exclusion.html",
"title": "Outlier Exclusion Vignette",
"author": "Olink DS team",
"engine": "knitr::rmarkdown",
"headings": [
"Introduction",
"PCA Plot",
"Overview of PCA Plot",
"How to use PCA plot to identify an outlier",
"PCA plot by panel",
"Labeling outliers",
"NPX Distribution Plot",
"Overview of NPX Distribution Plot",
"How to use NPX distribution plot to identify an outlier",
"QC Plot (IQR vs Sample Median)",
"Overview of QC Plot",
"How to use QC plot to identify an outlier",
"Interpreting and Handling Outliers",
"When should outliers be removed",
"Contact Us",
"Legal Disclaimer"
],
"created": "2026-06-08 16:32:12",
"modified": "2026-06-08 16:32:12",
"commits": 1
},
{
"source": "plate_randomizer.Rmd",
"filename": "plate_randomizer.html",
"title": "Plate Randomization Vignette",
"author": "Olink DS team",
"engine": "knitr::rmarkdown",
"headings": [
"Introduction",
"Sample randomization",
"Complete randomization",
"Generate randomization scheme that keeps subjects on the same plate",
"Multi-study manifests",
"Visualization",
"Plate layouts",
"Plate distribution",
"Data Output",
"Contact Us",
"Legal Disclaimer"
],
"created": "2026-06-08 16:32:12",
"modified": "2026-06-08 16:32:12",
"commits": 1
}
],
"_score": 2.6989700043360187,
"_indexed": false,
"_nocasepkg": "olinkanalyzevignettes",
"_universes": [
"cran",
"kathy-nevola",
"olink-proteomics"
],
"_indexurl": "https://kathy-nevola.r-universe.dev/OlinkAnalyzeVignettes",
"_binaries": [
{
"r": "4.7.0",
"os": "linux",
"version": "1.0.1",
"date": "2026-06-08T20:19:21.000Z",
"distro": "noble",
"commit": "c185521bb1030edb6b258dd72d0f168dd0c57c85",
"fileid": "486fe5c7aa63e68d3665aefb00a5f4a5067d33702c0f92e8e55fe094431a3da9",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/cran/actions/runs/27164152751"
},
{
"r": "4.6.0",
"os": "linux",
"version": "1.0.1",
"date": "2026-06-08T20:19:21.000Z",
"distro": "noble",
"commit": "c185521bb1030edb6b258dd72d0f168dd0c57c85",
"fileid": "2c763189d17a69213ab0ed329b384a74bc745191939a24b9e7830babe9f69b10",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/cran/actions/runs/27164152751"
},
{
"r": "4.6.0",
"os": "wasm",
"version": "1.0.1",
"date": "2026-06-08T20:19:21.000Z",
"commit": "c185521bb1030edb6b258dd72d0f168dd0c57c85",
"fileid": "2131c1024391929541451322d9544dc9a23eb10cef51632118b1de218ffe7dc9",
"status": "success",
"buildurl": "https://github.com/r-universe/cran/actions/runs/27164152751"
}
]
}