# Facilitate Analysis of Proteomic Data from Olink

## Documentation for package ‘OlinkAnalyze’ version 3.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

manifest | Example Sample Manifest
npx_data1 | NPX Data in Long format
npx_data2 | NPX Data in Long format, Follow-up
olink_anova | Function which performs an ANOVA per protein
olink_anova_posthoc | Function which performs an ANOVA posthoc test per protein.
olink_boxplot | Function which plots boxplots of selected variables
olink_bridgeselector | Bridge selection function
olink_color_discrete | Olink color scale for discrete ggplots
olink_color_gradient | Olink color scale for continuous ggplots
olink_displayPlateDistributions | Plot distributions of a given variable for all plates
olink_displayPlateLayout | Plot all plates colored by a variable
olink_dist_plot | Function to plot the NPX distribution by panel
olink_fill_discrete | Olink fill scale for discrete ggplots
olink_fill_gradient | Olink fill scale for continuous ggplots
olink_lmer | Function which performs a linear mixed model per protein
olink_lmer_plot | Function which performs a point-range plot per protein on a linear mixed model
olink_lmer_posthoc | Function which performs a linear mixed model posthoc per protein.
olink_normalization | Normalization of all proteins (by OlinkID).
olink_pal | Olink color panel for plotting
olink_pca_plot | Function to plot a PCA of the data
olink_plate_randomizer | Randomly assign samples to plates
olink_qc_plot | Function to plot an overview of a sample cohort per Panel
olink_ttest | Function which performs a t-test per protein
olink_volcano_plot | Easy volcano plot with Olink theme
read_NPX | Function to read NPX data into long format
set_plot_theme | Function to set plot theme