Package: OlinkAnalyzeVignettes 1.1.0

OlinkAnalyzeVignettes: Vignettes for Analyzing Data using 'OlinkAnalyze'

Exemplifying analysis of large-scale protein data from the 'Olink platform', primarily relative protein expression data that has been exported from 'Olink NPX Software', as well as QUANT data from 'Olink'. QUANT data is log-transformed. Materials focus on reading data, demonstrating 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 guide users extract biological insights from large-scale protein data run on the 'Olink platform'. More information on 'Olink' data can be found at <https://olink.com/>.

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], Stephen Pollo [aut], Kang Dong [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]

OlinkAnalyzeVignettes_1.1.0.tar.gz
OlinkAnalyzeVignettes_1.1.0.zip(r-4.7-any)OlinkAnalyzeVignettes_1.1.0.zip(r-4.6-any)OlinkAnalyzeVignettes_1.1.0.zip(r-4.5-any)
OlinkAnalyzeVignettes_1.1.0.tgz(r-4.6-any)OlinkAnalyzeVignettes_1.1.0.tgz(r-4.5-any)
OlinkAnalyzeVignettes_1.1.0.tar.gz(r-4.7-any)OlinkAnalyzeVignettes_1.1.0.tar.gz(r-4.6-any)
OlinkAnalyzeVignettes_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
OlinkAnalyzeVignettes/json (API)

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

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

On CRAN:

Conda:

3.00 score 282 downloads 1 exports 0 dependencies

Last updated from:194a0043f0. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK139
source / vignettesOK269
linux-releaseOK149
macos-releaseOK73
macos-oldrelOK98
windows-develOK79
windows-releaseOK58
windows-oldrelOK93
wasm-releaseOK126

Exports:open_docs

Dependencies:

Calculating LOD from Olink® NGS data
Introduction | Integrating LOD | Import Olink NGS datasets | A note on calculating LOD with clean_npx() | Integrating Negative Control LOD | A note on calculating LOD from counts | Integrating Fixed LOD | When to Use Fixed LOD vs NC LOD | Integrating Both NC LOD and Fixed LOD | Adjusting LOD for Intensity Normalized Data | Handling LOD in Bridge-Normalized Data | Export Olink NGS Data with LOD | Contact Us | Legal Disclaimer

Last update: 2026-10-09
Started: 2026-06-08

Introduction to bridging Olink® NPX datasets
Selecting bridge samples | Setup bridging datasets | Check bridging datasets | Bridging between two data sets | Perform bridging with non-matching sample names | Bridging evaluation | Export Bridged data | Contact Us | Legal Disclaimer

Last update: 2026-10-09
Started: 2026-06-08

Bridging across NGS-based Olink^®^ products
Introduction | Important Terminology | Within- and between-product bridging | Considerations for between-product bridging | Bridge Sample Selection | Workflow Overview | Import NPX files | Checking input datasets and bridging samples | Normalization | Determining bridging recommendations | Normalization using the median of paired differences | Quantile smoothing | Function Output | Evaluating the quality of bridging | Exporting Normalized Data | FAQs | Overlapping Assays within products | Downstream Analysis | Contact Us | Legal Disclaimer

Last update: 2026-06-08
Started: 2026-06-08

Outlier Exclusion Vignette
Introduction | PCA Plot | Overview of PCA Plot | How to use PCA plot to identify an outlier | PCA plot by panel | Labeling outliers | NPX Distribution Plot | Overview of NPX Distribution Plot | How to use NPX distribution plot to identify an outlier | QC Plot (IQR vs Sample Median) | Overview of QC Plot | How to use QC plot to identify an outlier | Interpreting and Handling Outliers | When should outliers be removed | Contact Us | Legal Disclaimer

Last update: 2026-06-08
Started: 2026-06-08

Plate Randomization Vignette
Introduction | Sample randomization | Complete randomization | Generate randomization scheme that keeps subjects on the same plate | Multi-study manifests | Visualization | Plate layouts | Plate distribution | Data Output | Contact Us | Legal Disclaimer

Last update: 2026-06-08
Started: 2026-06-08