├── .DS_Store ├── .Rbuildignore ├── .github ├── .DS_Store ├── .gitignore ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── pull_request_template.md └── workflows │ ├── CRAN_check.yaml │ ├── R-CMD-check.yaml │ ├── R-CMD-check_docker.yaml │ ├── R-CMD-check_hard.yaml │ ├── lint.yaml │ ├── matrix_config_check.json │ └── render-and-document.yaml ├── .gitignore ├── .lintr ├── LICENSE ├── LICENSE.md ├── OlinkAnalyze ├── .Rbuildignore ├── .gitignore ├── CITATION.cff ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── OlinkAnalyze.Rproj ├── R │ ├── Olink_anova.R │ ├── Olink_boxplot.R │ ├── Olink_bridgeselector.R │ ├── Olink_color.R │ ├── Olink_heatmap.R │ ├── Olink_one_non_parametric.R │ ├── Olink_ordinalRegression.R │ ├── Olink_plate_randomizer.R │ ├── Olink_theme.R │ ├── Olink_ttest.R │ ├── Olink_wilcox.R │ ├── Read_NPX_data.R │ ├── Volcano_plot.R │ ├── data.R │ ├── dist_plot.R │ ├── globals.R │ ├── linear_mixed_model.R │ ├── npxCheck.R │ ├── npxProcessing.R │ ├── npx_check_uniprot_dups.R │ ├── olink_Pathway_Enrichment.R │ ├── olink_Pathway_Heatmap.R │ ├── olink_Pathway_Visualization.R │ ├── olink_bridgeability_plot.R │ ├── olink_lod.R │ ├── olink_normalization.R │ ├── olink_normalization_n.R │ ├── olink_normalization_product.R │ ├── olink_normalization_utils.R │ ├── olink_outlier_detection_utils.R │ ├── olink_qc_plot.R │ ├── pca_plot.R │ ├── print_and_capture.R │ ├── read_flex.R │ ├── read_npx_csv.R │ ├── read_npx_parquet.R │ ├── read_npx_zip.R │ ├── sysdata.rda │ ├── umap_plot.R │ └── utils-pipe.R ├── cran-comments.md ├── data-raw │ ├── example_3k_data_small.R │ ├── example_HT_data_small.R │ ├── mapping.R │ ├── normalization_utils.R │ ├── sysdata.R │ └── tutorial_figures.R ├── data │ ├── manifest.rda │ ├── npx_data1.rda │ └── npx_data2.rda ├── inst │ ├── WORDLIST │ └── extdata │ │ ├── Example_NPX_Data.csv │ │ ├── Example_NPX_Data2_1.csv │ │ ├── Example_NPX_Data_3K.zip │ │ ├── Example_NPX_Data_empty.zip │ │ ├── Example_NPX_Data_sha256.zip │ │ ├── Example_NPX_Data_zip.zip │ │ ├── OlinkID_HT_mapping.rds │ │ ├── OlinkID_Reveal_HT_mapping.rds │ │ ├── OlinkID_Reveal_mapping.rds │ │ ├── complex_dataset.rds │ │ ├── npx_data1.xlsx │ │ ├── npx_data1_meta.csv │ │ ├── npx_data1_meta_original.csv │ │ ├── npx_data1_original.xlsx │ │ ├── npx_data2.xlsx │ │ ├── npx_data2_meta.csv │ │ ├── npx_data_ext.parquet │ │ ├── npx_data_ext_v1.zip │ │ ├── npx_data_ext_v2.zip │ │ └── npx_data_v3.zip ├── man │ ├── check_darid.Rd │ ├── check_data_completeness.Rd │ ├── check_lod_darid.Rd │ ├── figures │ │ ├── Bridging_schematic.png │ │ ├── Outlier_PCA.png │ │ ├── PCA_Outlier_Fig1.png │ │ ├── PCA_Panel.png │ │ ├── PCA_Treatment.png │ │ ├── PCA_btw_product_before.png │ │ ├── SCs_post_bridging.png │ │ ├── SCs_pre_bridging.png │ │ ├── assay_bridgeability.jpg │ │ ├── bridgeable_plt_MedianCenter.png │ │ ├── bridges_post_bridging.png │ │ ├── bridges_pre_bridging.png │ │ ├── bridging_results.rds │ │ ├── dist_boxplot.png │ │ ├── label_samples_pca.png │ │ ├── logo.html │ │ ├── olink_boxplot.png │ │ ├── olink_boxplot_anova_posthoc.png │ │ ├── olink_fill_discrete_boxplot.png │ │ ├── olink_heatmap_plot.png │ │ ├── olink_lmer_plot.png │ │ ├── olink_pathway_heatmap_gsea.png │ │ ├── olink_pathway_heatmap_ora.png │ │ ├── olink_umap_plot.png │ │ ├── olink_volcano_plot.png │ │ ├── outlier_line_pca.png │ │ ├── overlapping_samples_table.rds │ │ ├── qc_label_plot.png │ │ ├── qc_plot.png │ │ ├── qc_site_plot.png │ │ ├── sample_med_boxplot.png │ │ ├── set_plot_theme_boxplot.png │ │ ├── site_boxplot.png │ │ └── small_logo.png │ ├── manifest.Rd │ ├── mapping_file_id.Rd │ ├── norm_internal_adjust.Rd │ ├── norm_internal_adjust_not_ref.Rd │ ├── norm_internal_adjust_ref.Rd │ ├── norm_internal_assay_median.Rd │ ├── norm_internal_bridge.Rd │ ├── norm_internal_cross_product.Rd │ ├── norm_internal_reference_median.Rd │ ├── norm_internal_rename_cols.Rd │ ├── norm_internal_subset.Rd │ ├── norm_internal_update_maxlod.Rd │ ├── npx_data1.Rd │ ├── npx_data2.Rd │ ├── olink_anova.Rd │ ├── olink_anova_posthoc.Rd │ ├── olink_boxplot.Rd │ ├── olink_bridgeability_plot.Rd │ ├── olink_bridgeselector.Rd │ ├── olink_color_discrete.Rd │ ├── olink_color_gradient.Rd │ ├── olink_displayPlateDistributions.Rd │ ├── olink_displayPlateLayout.Rd │ ├── olink_dist_plot.Rd │ ├── olink_fill_discrete.Rd │ ├── olink_fill_gradient.Rd │ ├── olink_heatmap_plot.Rd │ ├── olink_iqr.Rd │ ├── olink_lmer.Rd │ ├── olink_lmer_plot.Rd │ ├── olink_lmer_posthoc.Rd │ ├── olink_lod.Rd │ ├── olink_median.Rd │ ├── olink_median_iqr_outlier.Rd │ ├── olink_norm_input_assay_overlap.Rd │ ├── olink_norm_input_check.Rd │ ├── olink_norm_input_check_df_cols.Rd │ ├── olink_norm_input_check_quant.Rd │ ├── olink_norm_input_check_samples.Rd │ ├── olink_norm_input_class.Rd │ ├── olink_norm_input_clean_assays.Rd │ ├── olink_norm_input_cross_product.Rd │ ├── olink_norm_input_norm_method.Rd │ ├── olink_norm_input_ref_medians.Rd │ ├── olink_norm_input_validate.Rd │ ├── olink_norm_product_id.Rd │ ├── olink_norm_reference_id.Rd │ ├── olink_normalization.Rd │ ├── olink_normalization_bridge.Rd │ ├── olink_normalization_bridgeable.Rd │ ├── olink_normalization_n.Rd │ ├── olink_normalization_n_check.Rd │ ├── olink_normalization_product_format.Rd │ ├── olink_normalization_project_name_check.Rd │ ├── olink_normalization_qs.Rd │ ├── olink_normalization_sample_check.Rd │ ├── olink_normalization_subset.Rd │ ├── olink_one_non_parametric.Rd │ ├── olink_one_non_parametric_posthoc.Rd │ ├── olink_ordinalRegression.Rd │ ├── olink_ordinalRegression_posthoc.Rd │ ├── olink_pal.Rd │ ├── olink_pathway_enrichment.Rd │ ├── olink_pathway_heatmap.Rd │ ├── olink_pathway_visualization.Rd │ ├── olink_pca_plot.Rd │ ├── olink_plate_randomizer.Rd │ ├── olink_qc_plot.Rd │ ├── olink_ttest.Rd │ ├── olink_umap_plot.Rd │ ├── olink_volcano_plot.Rd │ ├── olink_wilcox.Rd │ ├── pipe.Rd │ ├── print_and_capture.Rd │ ├── read_NPX.Rd │ ├── read_flex.Rd │ ├── read_npx_csv.Rd │ ├── read_npx_parquet.Rd │ ├── read_npx_zip.Rd │ └── set_plot_theme.Rd ├── tests │ ├── testthat.R │ └── testthat │ │ ├── _snaps │ │ ├── Olink_boxplot │ │ │ ├── boxplot-site-10prots.svg │ │ │ ├── boxplot-site-2prots.svg │ │ │ ├── boxplot-time-and-site.svg │ │ │ ├── boxplot-time-with-coloroption.svg │ │ │ └── boxplot-time.svg │ │ ├── Olink_plate_randomizer │ │ │ └── randomized-data.svg │ │ ├── Read_NPX_data.md │ │ ├── Volcano_plot │ │ │ ├── volcano-plot-with-coloroption.svg │ │ │ └── volcano-plot.svg │ │ ├── dist_plot │ │ │ ├── distribution-plot-col-by-treatment.svg │ │ │ └── distribution-plot.svg │ │ ├── linear_mixed_model │ │ │ ├── lmer-plot-more-prots-than-space.svg │ │ │ └── lmer-plot.svg │ │ ├── npxProcessing.md │ │ ├── olink_bridgeability_plot │ │ │ ├── bridgeable-plot-counts-oid40770.svg │ │ │ ├── bridgeable-plot-counts-oid40835.svg │ │ │ ├── bridgeable-plot-iqr-oid40770.svg │ │ │ ├── bridgeable-plot-iqr-oid40835.svg │ │ │ ├── bridgeable-plot-ks-oid40770.svg │ │ │ ├── bridgeable-plot-ks-oid40835.svg │ │ │ ├── bridgeable-plot-r2-oid40770.svg │ │ │ └── bridgeable-plot-r2-oid40835.svg │ │ └── olink_qc_plot │ │ │ ├── qc-plot-with-coloroption.svg │ │ │ └── qc-plot.svg │ │ ├── data │ │ ├── example_3k_data.R │ │ ├── example_3k_data.rds │ │ ├── example_HT_data.R │ │ ├── example_HT_data.rds │ │ ├── example_Reveal_data.rds │ │ ├── example_reveal_data.R │ │ ├── npx_data_format221010.RData │ │ ├── npx_data_format221121.RData │ │ ├── qq_normalization_reference_result.rds │ │ ├── qq_normalization_reference_result_reveal.rds │ │ ├── refResults.R │ │ ├── refResults.RData │ │ ├── ref_results_norm.R │ │ └── ref_results_norm.rds │ │ ├── helper-get_example_olink_data.R │ │ ├── refs │ │ ├── Flex_test_data_long_quant.xlsx │ │ └── mock_sampleID_hashes.csv │ │ ├── setup.R │ │ ├── test-Olink_anova.R │ │ ├── test-Olink_boxplot.R │ │ ├── test-Olink_bridgeselector.R │ │ ├── test-Olink_color.R │ │ ├── test-Olink_heatmap.R │ │ ├── test-Olink_one_non_parametric.R │ │ ├── test-Olink_ordinalRegression.R │ │ ├── test-Olink_plate_randomizer.R │ │ ├── test-Olink_ttest.R │ │ ├── test-Read_NPX_data.R │ │ ├── test-Volcano_plot.R │ │ ├── test-dist_plot.R │ │ ├── test-linear_mixed_model.R │ │ ├── test-npxProcessing.R │ │ ├── test-olink_Pathway_Enrichment.R │ │ ├── test-olink_Pathway_Heatmap.R │ │ ├── test-olink_Pathway_Visualization.R │ │ ├── test-olink_bridgeability_plot.R │ │ ├── test-olink_lod.R │ │ ├── test-olink_normalization.R │ │ ├── test-olink_normalization_n.R │ │ ├── test-olink_normalization_product.R │ │ ├── test-olink_normalization_utils.R │ │ ├── test-olink_qc_plot.R │ │ ├── test-pca_plot.R │ │ ├── test-print_and_capture.R │ │ ├── test-umap_plot.R │ │ └── test_Olink_wilcox.R └── vignettes │ ├── .gitignore │ ├── LOD.Rmd │ ├── OutlierExclusion.Rmd │ ├── Vignett.Rmd │ ├── bridging_crossproduct.Rmd │ ├── bridging_introduction.Rmd │ └── plate_randomizer.Rmd ├── OlinkRPackage.Rproj ├── README.Rmd ├── README.md ├── docker └── Dockerfile_for_tests └── figures ├── example_distplot.png ├── 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