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: 3.3.0
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: clusterProfiler, extrafont, FSA, ggplotify, here, knitr, markdown, msigdbr, openssl, ordinal, pheatmap, rmarkdown, scales, systemfonts, testthat (≥ 3.0.0), umap, vdiffr
Published: 2023-01-24
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), 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), Olink [cph, fnd]
Maintainer: Kathleen Nevola <biostattools at olink.com>
License: AGPL (≥ 3)
NeedsCompilation: no
Materials: NEWS
CRAN checks: OlinkAnalyze results

Documentation:

Reference manual: OlinkAnalyze.pdf
Vignettes: Olink® Analyze Vignette

Downloads:

Package source: OlinkAnalyze_3.3.0.tar.gz
Windows binaries: r-devel: OlinkAnalyze_3.2.2.zip, r-release: OlinkAnalyze_3.2.2.zip, r-oldrel: OlinkAnalyze_3.2.2.zip
macOS binaries: r-release (arm64): OlinkAnalyze_3.2.2.tgz, r-oldrel (arm64): OlinkAnalyze_3.2.2.tgz, r-release (x86_64): OlinkAnalyze_3.2.2.tgz, r-oldrel (x86_64): OlinkAnalyze_3.2.2.tgz
Old sources: OlinkAnalyze archive

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