Facilitate Analysis of Proteomic Data from Olink

check_data_completeness | Check data completeness |

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_heatmap_plot | Function to plot a heatmap of the NPX data |

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... |

olink_lmer_posthoc | Function which performs a linear mixed model posthoc per... |

olink_normalization | Normalization of all proteins (by OlinkID). |

olink_normalization_bridge | Bridge normalization of all proteins between two NPX... |

olink_normalization_n | Bridge and/or subset normalization of all proteins among... |

olink_normalization_n_check | An internal function to perform checks on the input of the... |

olink_normalization_project_name_check | An internal function to perform checks on the input project... |

olink_normalization_sample_check | An internal function to perform checks on the input samples... |

olink_normalization_subset | Subset normalization of all proteins between two NPX... |

olink_one_non_parametric | Function which performs a Kruskal-Wallis Test or Friedman... |

olink_one_non_parametric_posthoc | Function which performs posthoc test per protein for the... |

olink_ordinalRegression | Function which A two-way ordinal analysis of variance can... |

olink_ordinalRegression_posthoc | Function which performs an posthoc test per protein. |

olink_pal | Olink color panel for plotting |

olink_pathway_enrichment | Performs pathway enrichment using over-representation... |

olink_pathway_heatmap | Creates a heatmap of selected pathways and proteins |

olink_pathway_visualization | Creates bargraph of top/selected enrichment terms from GSEA... |

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_umap_plot | Function to make a UMAP plot from the data |

olink_volcano_plot | Easy volcano plot with Olink theme |

olink_wilcox | Function which performs a Mann-Whitney U Test per protein |

pipe | Pipe operator |

print_and_capture | Capture the output of printing an object |

read_flex | Read in flex data |

read_NPX | Function to read NPX data into long format |

read_npx_csv | Helper function to read in Olink Explore csv or txt files |

read_npx_parquet | Helper function to read in Olink Explore parquet output files |

read_npx_zip | Helper function to read in Olink Explore zip csv files |

set_plot_theme | Function to set plot theme |

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