Type: Package
Package: OlinkAnalyze
Title: Facilitate Analysis of Proteomic Data from Olink
Version: 5.1.0
Authors@R: c(
    person("Kathleen", "Nevola", , "biostattools@olink.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-5183-6444", "kathy-nevola")),
    person("Marianne", "Sandin", role = "aut",
           comment = c(ORCID = "0000-0001-6186-963X", "marisand")),
    person("Jamey", "Guess", role = "aut",
           comment = c(ORCID = "0000-0002-4017-0923", "jrguess")),
    person("Simon", "Forsberg", role = "aut",
           comment = c(ORCID = "0000-0002-7451-9222", "simfor")),
    person("Christoffer", "Cambronero", role = "aut",
           comment = c("Orbmac")),
    person("Pascal", "Pucholt", role = "aut",
           comment = c(ORCID = "0000-0003-3342-1373", "AskPascal")),
    person("Boxi", "Zhang", role = "aut",
           comment = c(ORCID = "0000-0001-7758-6204", "boxizhang")),
    person("Masoumeh", "Sheikhi", role = "aut",
           comment = c("MasoumehSheikhi")),
    person("Klev", "Diamanti", role = "aut",
           comment = c(ORCID = "0000-0002-4922-8415", "klevdiamanti")),
    person("Amrita", "Kar", role = "aut",
           comment = c("amrita-kar")),
    person("Lei", "Conze", role = "aut", 
            comment = c("leiliuC")),
    person("Kristyn", "Chin", role = "aut",
            comment = c("kristynchin-olink")),
    person("Danai", "Topouza", role = "aut",
            comment = c("dtopouza", ORCID = "0000-0002-6897-9281")),
    person("Stephen", "Pollo", role = "aut",
            comment = c("spollo-olprot", ORCID = "0000-0001-9252-4976")),
    person("Kang", "Dong", role = "aut",
            comment = c("KangD-dev", ORCID = "0000-0002-4567-5007")),
    person("Kristian", "Hodén", role = "aut",
           comment = c(ORCID = "0000-0003-0354-0662", "kristianHoden")),
    person("Per", "Eriksson", role = "ctb",
           comment = c(ORCID = "0000-0001-7633-403X", "b_watcher")),
    person("Nicola", "Moloney", role = "ctb",
            comment = c(ORCID = "0000-0003-4967-3284")),
    person("Britta", "Lötstedt", role = "ctb",
            comment = c(ORCID = "0000-0003-3545-5489")),
    person("Emmett", "Sprecher", role = "ctb",
           comment = c(ORCID = "0000-0002-7710-695X")),
    person("Jessica", "Barbagallo", role = "ctb",
           comment = c("jbarbagallo")),
    person("Olof", "Mansson", role = "ctr",
           comment = c("olofmansson")),
    person("Ola", "Caster", role = "ctb",
           comment = c("OlaCaster")),
    person("Olink", role = c("cph", "fnd"))
  )
Description: A collection of functions to facilitate analysis of
        proteomic data from Olink, primarily NPX data that has been
        exported from Olink Software. The functions also work on QUANT
        data from Olink by log- transforming the QUANT data. The
        functions are focused on reading data, facilitating data
        wrangling and quality control analysis, performing statistical
        analysis and generating figures to visualize the results of the
        statistical analysis. The goal of this package is to help users
        extract biological insights from proteomic data run on the
        Olink platform.
License: AGPL (>= 3)
Contact: biostattools@olink.com
URL: https://olink.com/
        https://github.com/Olink-Proteomics/OlinkRPackage
        https://7074596.fs1.hubspotusercontent-na1.net/hubfs/7074596/01-User%20Manuals%20for%20website/1494-Olink-Analyze-Cheatsheet.pdf
Config/testthat/edition: 3
Config/testthat/parallel: true
Config/testthat/start-first: olink_pathway_enrichment,
        olink_normalization, read_npx_legacy, read_npx_wide,
        olink_normalization_utils, olink_lmer,
        olink_ordinal_regression, olink_normalization_n,
        olink_normalization_format, pca_plot, read_npx_format,
        plot_is_bridgeable, clean_npx, plot_heatmap
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.1.0)
Imports: arrow (>= 14.0.0), cli (>= 3.6.2), data.table, dbplyr, dplyr
        (>= 1.2.0), duckdb, forcats, ggplot2, grDevices, pillar, rlang,
        stringr, tibble, tidyr
Suggests: broom, car, clusterProfiler, curl, emmeans, ggplotify,
        ggpubr, ggrepel, lme4, lmerTest, msigdbr (> 24.1.0), ordinal,
        readxl, pheatmap, scales, showtext, sysfonts, systemfonts,
        testthat (>= 3.3.0), vdiffr, withr, writexl, zip, umap,
        rstatix, FSA, kableExtra, knitr
VignetteBuilder: knitr
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: cmake libicu-dev libssl-dev xz-utils
Repository: https://olink-proteomics.r-universe.dev
Date/Publication: 2026-09-18 11:32:37 UTC
RemoteUrl: https://github.com/olink-proteomics/olinkrpackage
RemoteRef: HEAD
RemoteSha: 7385f477050b65e9470e709d30b1b23c6fcb5702
RemoteSubdir: OlinkAnalyze
NeedsCompilation: no
Packaged: 2026-10-18 11:10:50 UTC; root
Author: Kathleen Nevola [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5183-6444>, kathy-nevola),
  Marianne Sandin [aut] (ORCID: <https://orcid.org/0000-0001-6186-963X>,
    marisand),
  Jamey Guess [aut] (ORCID: <https://orcid.org/0000-0002-4017-0923>,
    jrguess),
  Simon Forsberg [aut] (ORCID: <https://orcid.org/0000-0002-7451-9222>,
    simfor),
  Christoffer Cambronero [aut] (Orbmac),
  Pascal Pucholt [aut] (ORCID: <https://orcid.org/0000-0003-3342-1373>,
    AskPascal),
  Boxi Zhang [aut] (ORCID: <https://orcid.org/0000-0001-7758-6204>,
    boxizhang),
  Masoumeh Sheikhi [aut] (MasoumehSheikhi),
  Klev Diamanti [aut] (ORCID: <https://orcid.org/0000-0002-4922-8415>,
    klevdiamanti),
  Amrita Kar [aut] (amrita-kar),
  Lei Conze [aut] (leiliuC),
  Kristyn Chin [aut] (kristynchin-olink),
  Danai Topouza [aut] (dtopouza, ORCID:
    <https://orcid.org/0000-0002-6897-9281>),
  Stephen Pollo [aut] (spollo-olprot, ORCID:
    <https://orcid.org/0000-0001-9252-4976>),
  Kang Dong [aut] (KangD-dev, ORCID:
    <https://orcid.org/0000-0002-4567-5007>),
  Kristian Hodén [aut] (ORCID: <https://orcid.org/0000-0003-0354-0662>,
    kristianHoden),
  Per Eriksson [ctb] (ORCID: <https://orcid.org/0000-0001-7633-403X>,
    b_watcher),
  Nicola Moloney [ctb] (ORCID: <https://orcid.org/0000-0003-4967-3284>),
  Britta Lötstedt [ctb] (ORCID: <https://orcid.org/0000-0003-3545-5489>),
  Emmett Sprecher [ctb] (ORCID: <https://orcid.org/0000-0002-7710-695X>),
  Jessica Barbagallo [ctb] (jbarbagallo),
  Olof Mansson [ctr] (olofmansson),
  Ola Caster [ctb] (OlaCaster),
  Olink [cph, fnd]
Maintainer: Kathleen Nevola <biostattools@olink.com>