Package: OlinkAnalyze 4.0.1

Kathleen Nevola

OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

A collection of functions to facilitate analysis of proteomic data from Olink, primarily NPX data that has been exported from Olink Software. The functions also work on QUANT data from Olink by log- transforming the QUANT data. The functions are focused on reading data, facilitating data wrangling and quality control analysis, performing statistical analysis and generating figures to visualize the results of the statistical analysis. The goal of this package is to help users extract biological insights from proteomic data run on the Olink platform.

Authors:Kathleen Nevola [aut, cre], Marianne Sandin [aut], Jamey Guess [aut], Simon Forsberg [aut], Christoffer Cambronero [aut], Pascal Pucholt [aut], Boxi Zhang [aut], Masoumeh Sheikhi [aut], Klev Diamanti [aut], Amrita Kar [aut], Lei Conze [aut], Kristyn Chin [aut], Danai Topouza [aut], Kristian Hodén [ctb], Per Eriksson [ctb], Nicola Moloney [ctb], Britta Lötstedt [ctb], Emmett Sprecher [ctb], Jessica Barbagallo [ctb], Olof Mansson [ctr], Ola Caster [ctb], Olink [cph, fnd]

OlinkAnalyze_4.0.1.tar.gz
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OlinkAnalyze.pdf |OlinkAnalyze.html✨
OlinkAnalyze/json (API)
NEWS

# Install 'OlinkAnalyze' in R:
install.packages('OlinkAnalyze', repos = c('https://olink-proteomics.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/olink-proteomics/olinkrpackage/issues

Datasets:

On CRAN:

olinkproteomicsproteomics-data-analysis

9.50 score 90 stars 63 scripts 1.2k downloads 38 exports 80 dependencies

Last updated 1 months agofrom:625707b376. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 24 2024
R-4.5-winOKOct 24 2024
R-4.5-linuxOKOct 24 2024
R-4.4-winOKOct 24 2024
R-4.4-macOKOct 24 2024
R-4.3-winOKOct 24 2024
R-4.3-macOKOct 24 2024

Exports:%>%olink_anovaolink_anova_posthocolink_boxplotolink_bridgeselectorolink_color_discreteolink_color_gradientolink_displayPlateDistributionsolink_displayPlateLayoutolink_dist_plotolink_fill_discreteolink_fill_gradientolink_heatmap_plotolink_lmerolink_lmer_plotolink_lmer_posthocolink_lodolink_normalizationolink_normalization_bridgeolink_normalization_nolink_normalization_subsetolink_one_non_parametricolink_one_non_parametric_posthocolink_ordinalRegressionolink_ordinalRegression_posthocolink_palolink_pathway_enrichmentolink_pathway_heatmapolink_pathway_visualizationolink_pca_plotolink_plate_randomizerolink_qc_plotolink_ttestolink_umap_plotolink_volcano_plotolink_wilcoxread_NPXset_plot_theme

Dependencies:abindbackportsbootbroomcarcarDatacellrangerclicolorspacecorrplotcowplotcpp11crayondata.tableDerivdoBydplyremmeansestimabilityfansifarverforcatsFormulagenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehmsisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpolynomprettyunitsprogresspurrrquantregR6RColorBrewerRcppRcppEigenreadxlrematchrlangrstatixscalesSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr

Bridging Olink^®^ Explore 3072 to Olink^®^ Explore HT

Rendered frombridging_E3072toEHT.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2024-09-23
Started: 2024-09-23

Calculating LOD from Olink® Explore data

Rendered fromLOD.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2024-08-06
Started: 2024-06-21

Introduction to bridging Olink® NPX datasets

Rendered frombridging_introduction.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2024-09-23
Started: 2023-04-26

Olink® Analyze Vignette

Olink DS team

Rendered fromVignett.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2024-09-23
Started: 2021-11-02

Outlier Exclusion Vignette

Olink DS team

Rendered fromOutlierExclusion.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2024-09-23
Started: 2023-04-26

Plate Randomization Vignette

Olink DS team

Rendered fromplate_randomizer.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2024-01-11
Started: 2023-04-26

Readme and manuals

Help Manual

Help pageTopics
Check data completenesscheck_data_completeness
Example Sample Manifestmanifest
Combine reference and non-reference datasetsnorm_internal_adjust
Add adjustment factors to a datasetnorm_internal_adjust_not_ref
Modify the reference dataset to be combined with the non-reference normalized datasetnorm_internal_adjust_ref
Compute median value of the quantification method for each Olink assaynorm_internal_assay_median
Internal bridge normalization functionnorm_internal_bridge
Internal function normalizing Olink Explore 3k to Olink Explore 3072norm_internal_cross_product
Internal reference median normalization functionnorm_internal_reference_median
Update column names of non-reference dataset based on those of reference datasetnorm_internal_rename_cols
Internal subset normalization functionnorm_internal_subset
NPX Data in Long formatnpx_data1
NPX Data in Long format, Follow-upnpx_data2
Function which performs an ANOVA per proteinolink_anova
Function which performs an ANOVA posthoc test per protein.olink_anova_posthoc
Function which plots boxplots of selected variablesolink_boxplot
Bridge selection functionolink_bridgeselector
Olink color scale for discrete ggplotsolink_color_discrete
Olink color scale for continuous ggplotsolink_color_gradient
Plot distributions of a given variable for all platesolink_displayPlateDistributions
Plot all plates colored by a variableolink_displayPlateLayout
Function to plot the NPX distribution by panelolink_dist_plot
Olink fill scale for discrete ggplotsolink_fill_discrete
Olink fill scale for continuous ggplotsolink_fill_gradient
Function to plot a heatmap of the NPX dataolink_heatmap_plot
Compute inter-quartile range (IQR) of multiplied by a fixed valueolink_iqr
Function which performs a linear mixed model per proteinolink_lmer
Function which performs a point-range plot per protein on a linear mixed modelolink_lmer_plot
Function which performs a linear mixed model posthoc per protein.olink_lmer_posthoc
Calculate LOD using Negative Controls or Fixed LODolink_lod
Compute median of quantified valueolink_median
Compute outliers based on median +/- iqr_sd * IQRolink_median_iqr_outlier
Check <datasets> and <reference_medians> for Olink identifiers not shared across datasets.olink_norm_input_assay_overlap
Check inputs of 'olink_normalization' function.olink_norm_input_check
Check columns of a list of datasets to be normalized.olink_norm_input_check_df_cols
Check reference samples to be used for normalizationolink_norm_input_check_samples
Check classes of input in olink_normalization functionolink_norm_input_class
Check <datasets> and <reference_medians> for unexpected Olink identifiers or excluded assaysolink_norm_input_clean_assays
Check if bridge or cross-platform normalizationolink_norm_input_cross_product
Check <datasets> and <reference_medians> for Olink identifiers not shared across datasets.olink_norm_input_norm_method
Check datasets of <reference_medians>olink_norm_input_ref_medians
Validate inputs of normalization functionolink_norm_input_validate
Normalize two Olink datasetsolink_normalization
Bridge normalization of all proteins between two NPX projects.olink_normalization_bridge
Identify if assays shared between Olink Explore 3072 and Olink Explore HT can be bridgedolink_normalization_bridgeable
Bridge and/or subset normalization of all proteins among multiple NPX projects.olink_normalization_n
An internal function to perform checks on the input of the function olink_normalization_n.olink_normalization_n_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_project_name_check
Quantile smoothing normalization of all proteins between two NPX projects.olink_normalization_qs
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_sample_check
Subset normalization of all proteins between two NPX projects.olink_normalization_subset
Function which performs a Kruskal-Wallis Test or Friedman Test per proteinolink_one_non_parametric
Function which performs posthoc test per protein for the results from Friedman or Kruskal-Wallis Test.olink_one_non_parametric_posthoc
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
Function which performs an posthoc test per protein.olink_ordinalRegression_posthoc
Olink color panel for plottingolink_pal
Performs pathway enrichment using over-representation analysis (ORA) or gene set enrichment analysis (GSEA)olink_pathway_enrichment
Creates a heatmap of selected pathways and proteinsolink_pathway_heatmap
Creates bargraph of top/selected enrichment terms from GSEA or ORA results from olink_pathway_enrichment()olink_pathway_visualization
Function to plot a PCA of the dataolink_pca_plot
Randomly assign samples to platesolink_plate_randomizer
Function to plot an overview of a sample cohort per Panelolink_qc_plot
Function which performs a t-test per proteinolink_ttest
Function to make a UMAP plot from the dataolink_umap_plot
Easy volcano plot with Olink themeolink_volcano_plot
Function which performs a Mann-Whitney U Test per proteinolink_wilcox
Capture the output of printing an objectprint_and_capture
Read in flex dataread_flex
Function to read NPX data into long formatread_NPX
Helper function to read in Olink Explore csv or txt filesread_npx_csv
Helper function to read in Olink Explore parquet output filesread_npx_parquet
Helper function to read in Olink Explore zip csv filesread_npx_zip
Function to set plot themeset_plot_theme