check_data_completeness
                        Check data completeness
manifest                Example Sample Manifest
norm_internal_adjust    Combine reference and non-reference datasets
norm_internal_adjust_not_ref
                        Add adjustment factors to a dataset
norm_internal_adjust_ref
                        Modify the reference dataset to be combined
                        with the non-reference normalized dataset
norm_internal_assay_median
                        Compute median value of the quantification
                        method for each Olink assay
norm_internal_bridge    Internal bridge normalization function
norm_internal_cross_product
                        Internal function normalizing Olink Explore 3k
                        to Olink Explore 3072
norm_internal_reference_median
                        Internal reference median normalization
                        function
norm_internal_rename_cols
                        Update column names of non-reference dataset
                        based on those of reference dataset
norm_internal_subset    Internal subset normalization function
norm_internal_update_maxlod
                        Update MaxLOD to the maximum MaxLOD across
                        normalized datasets.
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_bridgeability_plot
                        Plots for each bridgeable assays between two
                        products.
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_format_oid_no_overlap
                        Retrieve non-overlapping assays between two NPX
                        datasets
olink_format_rm_ext_ctrl
                        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_heatmap_plot      Function to plot a heatmap of the NPX data
olink_iqr               Compute inter-quartile range (IQR) of
                        multiplied by a fixed value
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_lod               Calculate LOD using Negative Controls or Fixed
                        LOD
olink_median            Compute median of quantified value
olink_median_iqr_outlier
                        Compute outliers based on median +/- iqr_sd *
                        IQR
olink_norm_input_assay_overlap
                        Check <datasets> and <reference_medians> for
                        Olink identifiers not shared across datasets.
olink_norm_input_check
                        Check inputs of 'olink_normalization' function.
olink_norm_input_check_df_cols
                        Check columns of a list of datasets to be
                        normalized.
olink_norm_input_check_quant
                        Check quantification columns.
olink_norm_input_check_samples
                        Check reference samples to be used for
                        normalization
olink_norm_input_class
                        Check classes of input in olink_normalization
                        function
olink_norm_input_clean_assays
                        Check <datasets> and <reference_medians> for
                        unexpected Olink identifiers or excluded assays
olink_norm_input_cross_product
                        Check if bridge or cross-platform normalization
olink_norm_input_norm_method
                        Check <datasets> and <reference_medians> for
                        Olink identifiers not shared across datasets.
olink_norm_input_ref_medians
                        Check datasets of <reference_medians>
olink_norm_input_validate
                        Validate inputs of normalization function
olink_norm_product_id   Identify names of product for each project
olink_norm_reference_id
                        Identify reference project.
olink_normalization     Normalize two Olink datasets
olink_normalization_bridge
                        Bridge normalization of all proteins between
                        two NPX projects.
olink_normalization_bridgeable
                        Identify if assays shared between Olink Explore
                        3072 and Olink Explore HT can be bridged
olink_normalization_format
                        Format the output of olink_normalization for
                        seamless use with downstream analysis
                        functions.
olink_normalization_n   Bridge and/or subset normalization of all
                        proteins among multiple NPX projects.
olink_normalization_n_check
                        An internal function to perform checks on the
                        input of the function olink_normalization_n.
olink_normalization_project_name_check
                        An internal function to perform checks on the
                        input project names in the functions
                        olink_normalization_bridge and
                        olink_normalization_subset. The function is
                        expected to run all checks on project names to
                        make sure that normalization can be performed
                        smoothly. It should work independently of the
                        function calling it.
olink_normalization_qs
                        Quantile smoothing normalization of all
                        proteins between two NPX projects.
olink_normalization_sample_check
                        An internal function to perform checks on the
                        input samples in the functions
                        olink_normalization_bridge and
                        olink_normalization_subset. The function is
                        expected to run all checks on SampleID to make
                        sure that normalization can be performed
                        smoothly. It should work independently of the
                        function calling it.
olink_normalization_subset
                        Subset normalization of all proteins between
                        two NPX projects.
olink_one_non_parametric
                        Function which performs a Kruskal-Wallis Test
                        or Friedman Test per protein
olink_one_non_parametric_posthoc
                        Function which performs posthoc test per
                        protein for the results from Friedman or
                        Kruskal-Wallis Test.
olink_ordinalRegression
                        Function which A two-way ordinal analysis of
                        variance can address an experimental design
                        with two independent variables, each of which
                        is a factor variable.  The main effect of each
                        independent variable can be tested, as well as
                        the effect of the interaction of the two
                        factors.
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 analysis (ORA) or gene set
                        enrichment analysis (GSEA)
olink_pathway_heatmap   Creates a heatmap of selected pathways and
                        proteins
olink_pathway_visualization
                        Creates bargraph of top/selected enrichment
                        terms from GSEA or ORA results from
                        olink_pathway_enrichment()
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
print_and_capture       Capture the output of printing an object
read_NPX                Function to read NPX data into long format
read_flex               Read in flex data
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
