Package: OlinkAnalyze 5.0.0

Kathleen Nevola

OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

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.

Authors:Kathleen Nevola [aut, cre], Marianne Sandin [aut], Jamey Guess [aut], Simon Forsberg [aut], Christoffer Cambronero [aut], Pascal Pucholt [aut], Boxi Zhang [aut], Masoumeh Sheikhi [aut], Klev Diamanti [aut], Amrita Kar [aut], Lei Conze [aut], Kristyn Chin [aut], Danai Topouza [aut], Stephen Pollo [aut], Kang Dong [aut], Kristian Hodén [ctb], Per Eriksson [ctb], Nicola Moloney [ctb], Britta Lötstedt [ctb], Emmett Sprecher [ctb], Jessica Barbagallo [ctb], Olof Mansson [ctr], Ola Caster [ctb], Olink [cph, fnd]

OlinkAnalyze_5.0.0.tar.gz
OlinkAnalyze_5.0.0.zip(r-4.7)OlinkAnalyze_5.0.0.zip(r-4.6)OlinkAnalyze_5.0.0.zip(r-4.5)
OlinkAnalyze_5.0.0.tgz(r-4.6-any)OlinkAnalyze_5.0.0.tgz(r-4.5-any)
OlinkAnalyze_5.0.0.tar.gz(r-4.7-any)OlinkAnalyze_5.0.0.tar.gz(r-4.6-any)
OlinkAnalyze_5.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
OlinkAnalyze/json (API)
NEWS

# Install 'OlinkAnalyze' in R:
install.packages('OlinkAnalyze', repos = c('https://olink-proteomics.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/olink-proteomics/olinkrpackage/issues

Datasets:

On CRAN:

Conda:

olinkproteomicsproteomics-data-analysis

10.21 score 130 stars 3 packages 115 scripts 2.0k downloads 47 exports 39 dependencies

Last updated from:5972c613ea. Checks:8 OK, 1 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK317
source / vignettesOK310
linux-release-x86_64OK312
macos-release-arm64OK333
macos-oldrel-arm64OK365
windows-develERROR174
windows-releaseOK284
windows-oldrelOK277
wasm-releaseOK189

Exports:check_npxclean_npxolink_anovaolink_anova_posthocolink_boxplotolink_bridge_selectorolink_bridgeability_plotolink_bridgeselectorolink_color_discreteolink_color_gradientolink_display_plate_distolink_display_plate_layoutolink_displayPlateDistributionsolink_displayPlateLayoutolink_dist_plotolink_fill_discreteolink_fill_gradientolink_heatmap_plotolink_lmerolink_lmer_plotolink_lmer_posthocolink_lodolink_normalizationolink_normalization_bridgeolink_normalization_nolink_normalization_subsetolink_one_non_parametricolink_one_non_parametric_posthocolink_ordinal_regressionolink_ordinal_regression_posthocolink_ordinalRegressionolink_ordinalRegression_posthocolink_osi_dist_plotolink_palolink_pathway_enrichmentolink_pathway_heatmapolink_pathway_visualizationolink_pca_plotolink_plate_randomizerolink_qc_plotolink_ttestolink_umap_plotolink_volcano_plotolink_wilcoxread_npxread_NPXset_plot_theme

Dependencies:arrowassertthatbitbit64blobclicpp11data.tableDBIdbplyrdplyrduckdbfarverforcatsgenericsggplot2gluegtableisobandlabelinglifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerrlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Olink® Analyze Vignette

Olink DS team

Rendered fromOlinkAnalyze-Vignette.Rmdusingknitr::rmarkdownon May 27 2026.

Last update: 2026-03-27
Started: 2026-03-27

Readme and manuals

Help Manual

Help pageTopics
assign subject to a plate for longitudinal randomizationassign_subject2plate
Help function to check if suggested libraries are installed when required.check_library_installed
Check NPX data formatcheck_npx
Clean proteomics data quantified with Olink's PEA technologyclean_npx
Example Sample Manifestmanifest
Combine reference and non-reference datasetsnorm_internal_adjust
Add adjustment factors to a datasetnorm_internal_adjust_not_ref
Modify the reference dataset to be combined with the non-reference normalized datasetnorm_internal_adjust_ref
Compute median value of the quantification method for each Olink assaynorm_internal_assay_median
Internal bridge normalization functionnorm_internal_bridge
Internal function normalizing Olink Explore 3k to Olink Explore 3072norm_internal_cross_product
Internal reference median normalization functionnorm_internal_reference_median
Update column names of non-reference dataset based on those of reference datasetnorm_internal_rename_cols
Internal subset normalization functionnorm_internal_subset
Update MaxLOD to the maximum MaxLOD across normalized datasets.norm_internal_update_maxlod
NPX Data in Long format.npx_data1
NPX Data in Long format, a follow-up.npx_data2
Function which performs an ANOVA per protein.olink_anova
Function which performs an ANOVA posthoc test per protein.olink_anova_posthoc
Function which plots boxplots of selected variablesolink_boxplot
Bridge selection functionolink_bridgeselector olink_bridge_selector
Plots for each bridgeable assays between two products.olink_bridgeability_plot
Olink color scale for discrete ggplotsolink_color_discrete
Olink color scale for continuous ggplotsolink_color_gradient
Plot distributions of a given variable for all platesolink_displayPlateDistributions olink_display_plate_dist
Plot all plates colored by a variableolink_displayPlateLayout olink_display_plate_layout
Function to plot the NPX distribution by panelolink_dist_plot
Olink fill scale for discrete ggplotsolink_fill_discrete
Olink fill scale for continuous ggplotsolink_fill_gradient
Retrieve non-overlapping assays between two NPX datasetsolink_format_oid_no_overlap
Remove negative controls and plate controls from dataset. For use in olink_normalization_format function. Generates a message stating which control samples were removed.olink_format_rm_ext_ctrl
Function to plot a heatmap of the NPX dataolink_heatmap_plot
Compute inter-quartile range (IQR) of multiplied by a fixed valueolink_iqr
Function that performs a linear mixed model per protein.olink_lmer
Function which performs a point-range plot per protein on a linear mixed modelolink_lmer_plot
Function which performs a linear mixed model posthoc per protein.olink_lmer_posthoc
Calculate LOD using Negative Controls or Fixed LODolink_lod
Compute median of quantified valueolink_median
Compute outliers based on median +/- iqr_sd * IQRolink_median_iqr_outlier
Check <datasets> and <reference_medians> for Olink identifiers not shared across datasets.olink_norm_input_assay_overlap
Check inputs of 'olink_normalization' function.olink_norm_input_check
Check columns of a list of datasets to be normalized.olink_norm_input_check_df_cols
Check reference samples to be used for normalizationolink_norm_input_check_samples
Check classes of input in olink_normalization functionolink_norm_input_class
Check <datasets> and <reference_medians> for unexpected Olink identifiers or excluded assaysolink_norm_input_clean_assays
Check if bridge or cross-platform normalizationolink_norm_input_cross_product
Check <datasets> and <reference_medians> for Olink identifiers not shared across datasets.olink_norm_input_norm_method
Check datasets of <reference_medians>olink_norm_input_ref_medians
Validate inputs of normalization functionolink_norm_input_validate
Identify names of product for each projectolink_norm_product_id
Identify reference project.olink_norm_reference_id
Normalize two Olink datasetsolink_normalization
Bridge normalization of all proteins between two NPX projects.olink_normalization_bridge
Identify if assays shared between Olink Explore 3072 and Olink Explore HT can be bridgedolink_normalization_bridgeable
Format the output of olink_normalization for seamless use with downstream analysis functions.olink_normalization_format
Bridge and/or subset normalization of all proteins among multiple NPX projects.olink_normalization_n
Quantile smoothing normalization of all proteins between two NPX projects.olink_normalization_qs
Subset normalization of all proteins between two NPX projects.olink_normalization_subset
Function which performs a Kruskal-Wallis Test or Friedman Test per proteinolink_one_non_parametric
Function which performs posthoc test per protein for the results from Friedman or Kruskal-Wallis Test.olink_one_non_parametric_posthoc
Function that performs a two-way ordinal analysis.olink_ordinalRegression olink_ordinal_regression
Function which performs an posthoc test per protein.olink_ordinalRegression_posthoc olink_ordinal_regression_posthoc
OSI distribution plotolink_osi_dist_plot
Olink color panel for plottingolink_pal
Performs pathway enrichment using over-representation analysis (ORA) or gene set enrichment analysis (GSEA)olink_pathway_enrichment
Creates a heatmap of proteins related to pathways using enrichment results from 'olink_pathway_enrichment'.olink_pathway_heatmap
Creates bargraph of top/selected enrichment terms from GSEA or ORA results from 'olink_pathway_enrichment'olink_pathway_visualization
Function to plot a PCA of the dataolink_pca_plot
Randomly assign samples to platesolink_plate_randomizer
Function to plot an overview of a sample cohort per Panel.olink_qc_plot
Function which performs a t-test per proteinolink_ttest
Function to make a UMAP plot from the dataolink_umap_plot
Easy volcano plot with Olink themeolink_volcano_plot
Function which performs a Mann-Whitney U Test per proteinolink_wilcox
Read Olink data in R.read_NPX read_npx
Function to set plot themeset_plot_theme