Installation | List of functions | Usage | Introduction to Olink NPX data format | Preprocessing | Read NPX data (read_NPX() or read_npx()) | Function arguments | Function output | Read multiple NPX data files (read_NPX() or 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 NGS NPX LOD (olink_lod()) | Statistical analysis | T-test analysis (olink_ttest()) | Mann-Whitney U Test analysis (olink_wilcox()) | Analysis of 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

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

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

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

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

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

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

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

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

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

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