{ "_id": "6a1692a6acfb0bcc41d78f94", "Type": "Package", "Package": "OlinkAnalyze", "Title": "Facilitate Analysis of Proteomic Data from Olink", "Version": "5.0.0", "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": "A collection of functions to facilitate analysis of\nproteomic data from Olink, primarily NPX data that has been\nexported from Olink Software. The functions also work on QUANT\ndata from Olink by log- transforming the QUANT data. The\nfunctions are focused on reading data, facilitating data\nwrangling and quality control analysis, performing statistical\nanalysis and generating figures to visualize the results of the\nstatistical analysis. The goal of this package is to help users\nextract biological insights from proteomic data run on the\nOlink platform.", "License": "AGPL (>= 3)", "Contact": "biostattools@olink.com", "URL": "https://olink.com/\nhttps://github.com/Olink-Proteomics/OlinkRPackage", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "Config/testthat/start-first": "read_npx_l*, read_npx_w*", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libicu-dev libssl-dev xz-utils", "Repository": "https://olink-proteomics.r-universe.dev", "Date/Publication": "2026-03-28 10:47:26 UTC", "RemoteUrl": "https://github.com/olink-proteomics/olinkrpackage", "RemoteRef": "HEAD", "RemoteSha": "5972c613eaf164dccae7fdcd33462856f36a1298", "RemoteSubdir": "OlinkAnalyze", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-27 06:36:48 UTC", "User": "root" }, "Author": "Kathleen Nevola [aut, cre] (ORCID:\n, kathy-nevola),\nMarianne Sandin [aut] (ORCID: ,\nmarisand),\nJamey Guess [aut] (ORCID: ,\njrguess),\nSimon Forsberg [aut] (ORCID: ,\nsimfor),\nChristoffer Cambronero [aut] (Orbmac),\nPascal Pucholt [aut] (ORCID: ,\nAskPascal),\nBoxi Zhang [aut] (ORCID: ,\nboxizhang),\nMasoumeh Sheikhi [aut] (MasoumehSheikhi),\nKlev Diamanti [aut] (ORCID: ,\nklevdiamanti),\nAmrita Kar [aut] (amrita-kar),\nLei Conze [aut] (leiliuC),\nKristyn Chin [aut] (kristynchin-olink),\nDanai Topouza [aut] (dtopouza, ORCID:\n),\nStephen Pollo [aut] (spollo-olprot, ORCID:\n),\nKang Dong [aut] (KangD-dev, ORCID:\n),\nKristian Hodén [ctb] (ORCID: ,\nkristianHoden),\nPer Eriksson [ctb] (ORCID: ,\nb_watcher),\nNicola Moloney [ctb] (ORCID: ),\nBritta Lötstedt [ctb] (ORCID: ),\nEmmett Sprecher [ctb] (ORCID: ),\nJessica Barbagallo [ctb] (jbarbagallo),\nOlof Mansson [ctr] (olofmansson),\nOla Caster [ctb] (OlaCaster),\nOlink [cph, fnd]", "Maintainer": "Kathleen Nevola ", "MD5sum": "7e2de73bc1a095c88cd09fa0b447f41e", 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"assign_subject2plate", "title": "assign subject to a plate for longitudinal randomization", "topics": [ "assign_subject2plate" ] }, { "page": "check_library_installed", "title": "Help function to check if suggested libraries are installed when required.", "topics": [ "check_library_installed" ] }, { "page": "check_npx", "title": "Check NPX data format", "topics": [ "check_npx" ] }, { "page": "clean_npx", "title": "Clean proteomics data quantified with Olink's PEA technology", "topics": [ "clean_npx" ] }, { "page": "manifest", "title": "Example Sample Manifest", "topics": [ "manifest" ] }, { "page": "norm_internal_adjust", "title": "Combine reference and non-reference datasets", "topics": [ "norm_internal_adjust" ] }, { "page": "norm_internal_adjust_not_ref", "title": "Add adjustment factors to a dataset", "topics": [ "norm_internal_adjust_not_ref" ] }, { "page": "norm_internal_adjust_ref", "title": "Modify the reference dataset to be combined with the non-reference normalized dataset", "topics": [ "norm_internal_adjust_ref" ] }, { "page": "norm_internal_assay_median", "title": "Compute median value of the quantification method for each Olink assay", "topics": [ "norm_internal_assay_median" ] }, { "page": "norm_internal_bridge", "title": "Internal bridge normalization function", "topics": [ "norm_internal_bridge" ] }, { "page": "norm_internal_cross_product", "title": "Internal function normalizing Olink Explore 3k to Olink Explore 3072", "topics": [ "norm_internal_cross_product" ] }, { "page": "norm_internal_reference_median", "title": "Internal reference median normalization function", "topics": [ "norm_internal_reference_median" ] }, { "page": "norm_internal_rename_cols", "title": "Update column names of non-reference dataset based on those of reference dataset", "topics": [ "norm_internal_rename_cols" ] }, { "page": "norm_internal_subset", "title": "Internal subset normalization function", "topics": [ "norm_internal_subset" ] }, { "page": "norm_internal_update_maxlod", "title": "Update MaxLOD to the maximum MaxLOD across normalized datasets.", "topics": [ "norm_internal_update_maxlod" ] }, { "page": "npx_data1", "title": "NPX Data in Long format.", "topics": [ "npx_data1" ] }, { "page": "npx_data2", "title": "NPX Data in Long format, a follow-up.", "topics": [ "npx_data2" ] }, { "page": "olink_anova", "title": "Function which performs an ANOVA per protein.", "topics": [ "olink_anova" ] }, { "page": "olink_anova_posthoc", "title": "Function which performs an ANOVA posthoc test per protein.", "topics": [ "olink_anova_posthoc" ] }, { "page": "olink_boxplot", "title": "Function which plots boxplots of selected variables", "topics": [ "olink_boxplot" ] }, { "page": "olink_bridge_selector", "title": "Bridge selection function", "topics": [ "olink_bridgeselector", "olink_bridge_selector" ] }, { "page": "olink_bridgeability_plot", "title": "Plots for each bridgeable assays between two products.", "topics": [ "olink_bridgeability_plot" ] }, { "page": "olink_color_discrete", "title": "Olink color scale for discrete ggplots", "topics": [ "olink_color_discrete" ] }, { "page": "olink_color_gradient", "title": "Olink color scale for continuous ggplots", "topics": [ "olink_color_gradient" ] }, { "page": "olink_display_plate_dist", "title": "Plot distributions of a given variable for all plates", "topics": [ "olink_displayPlateDistributions", "olink_display_plate_dist" ] }, { "page": "olink_display_plate_layout", "title": "Plot all plates colored by a variable", "topics": [ "olink_displayPlateLayout", "olink_display_plate_layout" ] }, { "page": "olink_dist_plot", "title": "Function to plot the NPX distribution by panel", "topics": [ "olink_dist_plot" ] }, { "page": "olink_fill_discrete", "title": "Olink fill scale for discrete ggplots", "topics": [ "olink_fill_discrete" ] }, { "page": "olink_fill_gradient", "title": "Olink fill scale for continuous ggplots", "topics": [ "olink_fill_gradient" ] }, { "page": "olink_format_oid_no_overlap", "title": "Retrieve non-overlapping assays between two NPX datasets", "topics": [ "olink_format_oid_no_overlap" ] }, { "page": "olink_format_rm_ext_ctrl", "title": "Remove negative controls and plate controls from dataset. For use in olink_normalization_format function. Generates a message stating which control samples were removed.", "topics": [ "olink_format_rm_ext_ctrl" ] }, { "page": "olink_heatmap_plot", "title": "Function to plot a heatmap of the NPX data", "topics": [ "olink_heatmap_plot" ] }, { "page": "olink_iqr", "title": "Compute inter-quartile range (IQR) of multiplied by a fixed value", "topics": [ "olink_iqr" ] }, { "page": "olink_lmer", "title": "Function that performs a linear mixed model per protein.", "topics": [ "olink_lmer" ] }, { "page": "olink_lmer_plot", "title": "Function which performs a point-range plot per protein on a linear mixed model", "topics": [ "olink_lmer_plot" ] }, { "page": "olink_lmer_posthoc", "title": "Function which performs a linear mixed model posthoc per protein.", "topics": [ "olink_lmer_posthoc" ] }, { "page": "olink_lod", "title": "Calculate LOD using Negative Controls or Fixed LOD", "topics": [ "olink_lod" ] }, { "page": "olink_median", "title": "Compute median of quantified value", "topics": [ "olink_median" ] }, { "page": "olink_median_iqr_outlier", "title": "Compute outliers based on median +/- iqr_sd * IQR", "topics": [ "olink_median_iqr_outlier" ] }, { "page": "olink_norm_input_assay_overlap", "title": "Check and for Olink identifiers not shared across datasets.", "topics": [ "olink_norm_input_assay_overlap" ] }, { "page": "olink_norm_input_check", "title": "Check inputs of 'olink_normalization' function.", "topics": [ "olink_norm_input_check" ] }, { "page": "olink_norm_input_check_df_cols", "title": "Check columns of a list of datasets to be normalized.", "topics": [ "olink_norm_input_check_df_cols" ] }, { "page": "olink_norm_input_check_samples", "title": "Check reference samples to be used for normalization", "topics": [ "olink_norm_input_check_samples" ] }, { "page": "olink_norm_input_class", "title": "Check classes of input in olink_normalization function", "topics": [ "olink_norm_input_class" ] }, { "page": "olink_norm_input_clean_assays", "title": "Check and for unexpected Olink identifiers or excluded assays", "topics": [ "olink_norm_input_clean_assays" ] }, { "page": "olink_norm_input_cross_product", "title": "Check if bridge or cross-platform normalization", "topics": [ "olink_norm_input_cross_product" ] }, { "page": "olink_norm_input_norm_method", "title": "Check and for Olink identifiers not shared across datasets.", "topics": [ "olink_norm_input_norm_method" ] }, { "page": "olink_norm_input_ref_medians", "title": "Check datasets of ", "topics": [ "olink_norm_input_ref_medians" ] }, { "page": "olink_norm_input_validate", "title": "Validate inputs of normalization function", "topics": [ "olink_norm_input_validate" ] }, { "page": "olink_norm_product_id", "title": "Identify names of product for each project", "topics": [ "olink_norm_product_id" ] }, { "page": "olink_norm_reference_id", "title": "Identify reference project.", "topics": [ "olink_norm_reference_id" ] }, { "page": "olink_normalization", "title": "Normalize two Olink datasets", "topics": [ "olink_normalization" ] }, { "page": "olink_normalization_bridge", "title": "Bridge normalization of all proteins between two NPX projects.", "topics": [ "olink_normalization_bridge" ] }, { "page": "olink_normalization_bridgeable", "title": "Identify if assays shared between Olink Explore 3072 and Olink Explore HT can be bridged", "topics": [ "olink_normalization_bridgeable" ] }, { "page": "olink_normalization_format", "title": "Format the output of olink_normalization for seamless use with downstream analysis functions.", "topics": [ "olink_normalization_format" ] }, { "page": "olink_normalization_n", "title": "Bridge and/or subset normalization of all proteins among multiple NPX projects.", "topics": [ "olink_normalization_n" ] }, { "page": "olink_normalization_qs", "title": "Quantile smoothing normalization of all proteins between two NPX projects.", "topics": [ "olink_normalization_qs" ] }, { "page": "olink_normalization_subset", "title": "Subset normalization of all proteins between two NPX projects.", "topics": [ "olink_normalization_subset" ] }, { "page": "olink_one_non_parametric", "title": "Function which performs a Kruskal-Wallis Test or Friedman Test per protein", "topics": [ "olink_one_non_parametric" ] }, { "page": "olink_one_non_parametric_posthoc", "title": "Function which performs posthoc test per protein for the results from Friedman or Kruskal-Wallis Test.", "topics": [ "olink_one_non_parametric_posthoc" ] }, { "page": "olink_ordinal_regression", "title": "Function that performs a two-way ordinal analysis.", "topics": [ "olink_ordinalRegression", "olink_ordinal_regression" ] }, { "page": "olink_ordinal_regression_posthoc", "title": "Function which performs an posthoc test per protein.", "topics": [ "olink_ordinalRegression_posthoc", "olink_ordinal_regression_posthoc" ] }, { "page": "olink_osi_dist_plot", "title": "OSI distribution plot", "topics": [ "olink_osi_dist_plot" ] }, { "page": "olink_pal", "title": "Olink color panel for plotting", "topics": [ "olink_pal" ] }, { "page": "olink_pathway_enrichment", "title": "Performs pathway enrichment using over-representation analysis (ORA) or gene set enrichment analysis (GSEA)", "topics": [ "olink_pathway_enrichment" ] }, { "page": "olink_pathway_heatmap", "title": "Creates a heatmap of proteins related to pathways using enrichment results from 'olink_pathway_enrichment'.", "topics": [ "olink_pathway_heatmap" ] }, { "page": "olink_pathway_visualization", "title": "Creates bargraph of top/selected enrichment terms from GSEA or ORA results from 'olink_pathway_enrichment'", "topics": [ "olink_pathway_visualization" ] }, { "page": "olink_pca_plot", "title": "Function to plot a PCA of the data", "topics": [ "olink_pca_plot" ] }, { "page": "olink_plate_randomizer", "title": "Randomly assign samples to plates", "topics": [ "olink_plate_randomizer" ] }, { "page": "olink_qc_plot", "title": "Function to plot an overview of a sample cohort per Panel.", "topics": [ "olink_qc_plot" ] }, { "page": "olink_ttest", "title": "Function which performs a t-test per protein", "topics": [ "olink_ttest" ] }, { "page": "olink_umap_plot", "title": "Function to make a UMAP plot from the data", "topics": [ "olink_umap_plot" ] }, { "page": "olink_volcano_plot", "title": "Easy volcano plot with Olink theme", "topics": [ "olink_volcano_plot" ] }, { "page": "olink_wilcox", "title": "Function which performs a Mann-Whitney U Test per protein", "topics": [ "olink_wilcox" ] }, { "page": "read_npx", "title": "Read Olink data in R.", "topics": [ "read_NPX", "read_npx" ] }, { "page": "set_plot_theme", "title": "Function to set plot theme", "topics": [ "set_plot_theme" ] } ], "_readme": "https://github.com/olink-proteomics/olinkrpackage/raw/HEAD/README.md", "_rundeps": [ "arrow", "assertthat", "bit", "bit64", "blob", "cli", "cpp11", "data.table", "DBI", "dbplyr", "dplyr", "duckdb", "farver", "forcats", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "OlinkAnalyze-Vignette.Rmd", "filename": "OlinkAnalyze-Vignette.html", "title": "Olink® Analyze Vignette", "author": "Olink DS team", "engine": "knitr::rmarkdown", "headings": [ "Installation", "List of functions", "Usage", "Introduction to Olink NPX data format", "Preprocessing", "Read NPX data (read_NPX)", "Function arguments", "Function output", "Read multiple NPX data files (read_NPX)", "Check NPX data quality (check_npx)", "Clean NPX data (clean_npx)", "Randomize samples on plate (olink_plate_randomizer)", "Select bridge samples (olink_bridgeselector)", "Normalizing NPX data (olink_normalization)", "Integrating Explore NPX LOD (olink_lod)", "Statistical analysis", "T-test analysis (olink_ttest)", "Mann-Whitney U Test analysis (olink_wilcox)", "Analysis for variance (ANOVA) (olink_anova)", "Post-hoc ANOVA analysis (olink_anova_posthoc)", "Linear mixed effects model analysis (olink_lmer)", "Function outcome", "Post-hoc linear mixed effects model analysis (olink_lmer_posthoc)", "Additional Statistical Tests", "Pathway Enrichment (olink_pathway_enrichment)", "Function Arguments", "Function Output", "Exploratory analysis", "Principal components analysis (PCA) plot (olink_pca_plot)", "Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) (olink_umap_plot)", "Function arguments (selection)", "Visualization", "Boxplots for outcomes (olink_boxplot)", "Boxplots for QC (olink_dist_plot)", "Point-range plot for LMER (olink_lmer_plot)", "Heatmap for visualizing pathway enrichment (olink_pathway_heatmap)", "Bargraph for visualizing pathway enrichment (olink_pathway_visualization)", "Scatterplot for QC (olink_qc_plot)", "Heatmap (olink_heatmap_plot)", "Plot results of t-test (olink_volcano_plot)", "Theming function (set_plot_theme)", "Color theming (olink_color_discrete, olink_color_gradient, olink_fill_discrete, olink_fill_gradient)", "Visualizing bridgeability criteria for between-product normalization (olink_bridgeability_plot)", "Contact Us", "Legal Disclaimer" ], "created": "2026-03-27 19:58:58", "modified": "2026-03-27 19:58:58", "commits": 1 } ], "_score": 10.214744875888224, "_indexed": true, "_nocasepkg": "olinkanalyze", "_universes": [ "olink-proteomics", "kathy-nevola" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "5.0.0", "date": "2026-05-27T06:40:26.000Z", "distro": "noble", "commit": "5972c613eaf164dccae7fdcd33462856f36a1298", "fileid": "5c5041e141a7ad239a7468397daa6c8f9dee47972dc7f64dc13719ce57756fee", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/olink-proteomics/actions/runs/26494924223" }, { "r": "4.6.0", "os": "linux", "version": "5.0.0", "date": "2026-05-27T06:40:21.000Z", "distro": "noble", "commit": 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