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.

Version: 3.8.2
Depends: R (≥ 4.1.0)
Imports: broom, car, dplyr, emmeans, forcats, generics, ggplot2, ggpubr, ggrepel, grDevices, grid, lme4, lmerTest, magrittr, methods, readxl, rlang, rstatix, stats, stringr, tibble, tidyr, tidyselect, tools, utils, zip
Suggests: arrow, clusterProfiler, extrafont, FSA, ggplotify, here, kableExtra, knitr, markdown, msigdbr, openssl, ordinal, pheatmap, rmarkdown, scales, systemfonts, testthat (≥ 3.0.0), umap, vdiffr
Published: 2024-06-27
DOI: 10.32614/CRAN.package.OlinkAnalyze
Author: Kathleen Nevola ORCID iD [aut, cre] (kathy-nevola), Marianne Sandin ORCID iD [aut] (marisand), Jamey Guess ORCID iD [aut] (jrguess), Simon Forsberg ORCID iD [aut] (simfor), Christoffer Cambronero [aut] (Orbmac), Pascal Pucholt ORCID iD [aut] (AskPascal), Boxi Zhang ORCID iD [aut] (boxizhang), Masoumeh Sheikhi [aut] (MasoumehSheikhi), Klev Diamanti ORCID iD [aut] (klevdiamanti), Amrita Kar [aut] (amrita-kar), Lei Conze [aut] (leiliuC), Kristyn Chin [aut] (kristynchin-olink), Kristian Hodén ORCID iD [ctb] (kristianHoden), Per Eriksson ORCID iD [ctb] (b_watcher), Nicola Moloney ORCID iD [ctb], Britta Lötstedt ORCID iD [ctb], Emmett Sprecher ORCID iD [ctb], Jessica Barbagallo [ctb] (jbarbagallo), Olof Mansson [ctr] (olofmansson), Ola Caster [ctb] (OlaCaster), Danai Topouza ORCID iD [ctb] (dtopouza), Olink [cph, fnd]
Maintainer: Kathleen Nevola <biostattools at olink.com>
Contact: biostattools@olink.com
License: AGPL (≥ 3)
URL: https://olink.com/ https://github.com/Olink-Proteomics/OlinkRPackage
NeedsCompilation: no
Materials: NEWS
CRAN checks: OlinkAnalyze results


Reference manual: OlinkAnalyze.pdf
Vignettes: Calculating LOD from Olink® Explore data
Outlier Exclusion Vignette
Olink® Analyze Vignette
Introduction to bridging Olink® NPX datasets
Plate Randomization Vignette


Package source: OlinkAnalyze_3.8.2.tar.gz
Windows binaries: r-devel: OlinkAnalyze_3.8.2.zip, r-release: OlinkAnalyze_3.8.2.zip, r-oldrel: OlinkAnalyze_3.8.2.zip
macOS binaries: r-release (arm64): OlinkAnalyze_3.8.2.tgz, r-oldrel (arm64): OlinkAnalyze_3.8.2.tgz, r-release (x86_64): OlinkAnalyze_3.8.2.tgz, r-oldrel (x86_64): OlinkAnalyze_3.8.2.tgz
Old sources: OlinkAnalyze archive

Reverse dependencies:

Reverse suggests: autonomics


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