Man pages for OlinkAnalyze
Facilitate Analysis of Proteomic Data from Olink

check_data_completenessCheck data completeness
manifestExample Sample Manifest
npx_data1NPX Data in Long format
npx_data2NPX Data in Long format, Follow-up
olink_anovaFunction which performs an ANOVA per protein
olink_anova_posthocFunction which performs an ANOVA posthoc test per protein.
olink_boxplotFunction which plots boxplots of selected variables
olink_bridgeselectorBridge selection function
olink_color_discreteOlink color scale for discrete ggplots
olink_color_gradientOlink color scale for continuous ggplots
olink_displayPlateDistributionsPlot distributions of a given variable for all plates
olink_displayPlateLayoutPlot all plates colored by a variable
olink_dist_plotFunction to plot the NPX distribution by panel
olink_fill_discreteOlink fill scale for discrete ggplots
olink_fill_gradientOlink fill scale for continuous ggplots
olink_heatmap_plotFunction to plot a heatmap of the NPX data
olink_lmerFunction which performs a linear mixed model per protein
olink_lmer_plotFunction which performs a point-range plot per protein on a...
olink_lmer_posthocFunction which performs a linear mixed model posthoc per...
olink_normalizationNormalization of all proteins (by OlinkID).
olink_normalization_bridgeBridge normalization of all proteins between two NPX...
olink_normalization_nBridge and/or subset normalization of all proteins among...
olink_normalization_n_checkAn internal function to perform checks on the input of the...
olink_normalization_project_name_checkAn internal function to perform checks on the input project...
olink_normalization_sample_checkAn internal function to perform checks on the input samples...
olink_normalization_subsetSubset normalization of all proteins between two NPX...
olink_one_non_parametricFunction which performs a Kruskal-Wallis Test or Friedman...
olink_one_non_parametric_posthocFunction which performs posthoc test per protein for the...
olink_ordinalRegressionFunction which A two-way ordinal analysis of variance can...
olink_ordinalRegression_posthocFunction which performs an posthoc test per protein.
olink_palOlink color panel for plotting
olink_pathway_enrichmentPerforms pathway enrichment using over-representation...
olink_pathway_heatmapCreates a heatmap of selected pathways and proteins
olink_pathway_visualizationCreates bargraph of top/selected enrichment terms from GSEA...
olink_pca_plotFunction to plot a PCA of the data
olink_plate_randomizerRandomly assign samples to plates
olink_qc_plotFunction to plot an overview of a sample cohort per Panel
olink_ttestFunction which performs a t-test per protein
olink_umap_plotFunction to make a UMAP plot from the data
olink_volcano_plotEasy volcano plot with Olink theme
olink_wilcoxFunction which performs a Mann-Whitney U Test per protein
pipePipe operator
print_and_captureCapture the output of printing an object
read_flexRead in flex data
read_NPXFunction to read NPX data into long format
read_npx_csvHelper function to read in Olink Explore csv or txt files
read_npx_parquetHelper function to read in Olink Explore parquet output files
read_npx_zipHelper function to read in Olink Explore zip csv files
set_plot_themeFunction to set plot theme
OlinkAnalyze documentation built on Nov. 4, 2023, 1:07 a.m.