R Observatory: Metrics for OlinkAnalyze version 5.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

OlinkAnalyze

5.1.0Package record

Facilitate Analysis of Proteomic Data from Olink

0packages dependsuggested by 1

20.7Kdownloads / year

52.1%test coverage

13/13flavors OK

Overview

About

Maintained by Kathleen NevolaCRAN page ↗GitHub ↗Website ↗Declared funder: 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.

Changes in 5.1.0

Minor Changes

improved QC warning flag summation (@klevdiamanti, #781)
new S3 object and ArrowObject connecting NPX data with check log allowing users to skip running check_npx() explicitly (@klevdiamanti, #765, #785, #786)

Bug Fix

improved logic for determining if file is wide or long (@klevdiamanti, #773)
grammar fixed in error message when column is missing (@klevdiamanti, #780)
read_npx wide format data error message clarified (@klevdiamanti, #782)
refactoring of check_npx to use list-style subsetting (@klevdiamanti, #784)
Update tests to accommodate updated precision of adjusted p-values in rstatix v1.0.0 (@klevdiamanti, #774 )
Swap the legacy .Dim for the newer dim argument in the function structure() (@klevdiamanti, #783)

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("OlinkAnalyze", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("Olink-Proteomics/OlinkRPackage")

Development version from Olink-Proteomics/OlinkRPackage. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-olinkanalyze

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-OlinkAnalyze

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-OlinkAnalyze

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 11.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-30
ERROR8 OK, 4 NOTE, 1 ERROR2026-09-04
NOTE8 OK, 5 NOTE2026-08-12
ERROR7 OK, 5 NOTE, 1 ERROR2026-08-09
NOTE8 OK, 5 NOTE2026-07-22

Show 13 earlier changesHide 13 earlier changes

ERROR9 OK, 4 ERROR2026-07-11
OK13 OK2026-06-20
ERROR12 OK, 1 ERROR2026-06-17
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-24
ERROR12 OK, 1 ERROR2026-05-17
OK13 OK2026-05-15
ERROR12 OK, 1 ERROR2026-05-13
OK13 OK2026-05-04
ERROR12 OK, 1 ERROR2026-05-03
OK14 OK2026-03-29
NOTE13 OK, 1 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 5.1.0

READMENoVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 5.1.0Citation fileNoWebsiteYes

Help pages: 147 (74 internal)
Examples that run: 0%43 only when donttest examples are enabled (R CMD check --as-cran) · 6 never run
Exported functions with examples: 98%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 1%

Vignettes (1)

Olink® Analyze Vignette

How these are measured

Downloads

20.7K

CRAN downloads in the past year

Rank #2,839 · ~57/day · ~1.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.9K30 days

5.1K90 days

20.7K1 year

Compare downloads with other packages →

Also on230 r2u11 autocran2.6K conda_forge

How downloads are counted

Repository

olink-proteomics/olinkrpackage ↗Organization: Olink-Proteomics

140Stars

38Forks

3Open issues

2Open PRs

38Releases

3,453Commits

30Commit identities

olinkproteomicsproteomics-data-analysisrrstats

License file reads as AGPL-3.0 · 3,453 commits · Last activity 2026-09-18 · +1.4% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 85%
Median days to close, 50 most recently updated closed issues: 7
Median days to close, 50 most recently updated closed PRs: 7

Stars over time

2025-10-15 · 1192026-10-06 · 140

How these are measured

PracticesBeta

10 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/olink-proteomics/olinkrpackage on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (2)

Issue templatesPR template

Docs source (1)

README.Rmd

Automation and maintenance (1)

Dependabot

Show all practicesHide 2 practices

Lint, format, editor (3)

lintrLint workflowRStudio project

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v3 (2026-09-26)

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2026-02-10
Pull request: opened by its own account
Commits: 4 by its own account

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

41 external dependencies (excludes base and recommended)

Installing OlinkAnalyze adds 39 packages (20 with compiled code, 45 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.1.0

Imports (14)

arrow cli data.table dbplyr dplyr duckdb forcats ggplot2grDevicespillar rlang stringr tibble tidyr

LinkingTo (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

OlinkAnalyzeVignettes

How these are counted

Code & Tests

Datasets

People & History

People (24)

Kathleen Nevola

Author, Maintainer since 3.0.0 (2022)

kathy-nevola

Christoffer Cambronero

Author

Orbmac

Kristyn Chin

Author · added in 3.7.0

kristynchin-olink

Lei Conze

Author · added in 3.4.0

leiliuC

Klev Diamanti

Author

klevdiamanti

Kang Dong

Author · added in 4.2.0

KangD-dev

Simon Forsberg

Author

simfor

Jamey Guess

Author

jrguess

Kristian Hodén

Author · added in 3.1.0

kristianHoden

Amrita Kar

Author · added in 3.3.0

amrita-kar

Stephen Pollo

Author · added in 4.2.0

spollo-olprot

Pascal Pucholt

Author

AskPascal

Marianne Sandin

Author

marisand

Masoumeh Sheikhi

Author · added in 3.1.0

MasoumehSheikhi

Danai Topouza

Author · added in 3.8.2

dtopouza

Boxi Zhang

Author

boxizhang

Jessica Barbagallo

Contributor

jbarbagallo

Ola Caster

Contributor

OlaCaster

Per Eriksson

Contributor

b_watcher

Britta Lötstedt

Contributor · added in 3.3.0

Nicola Moloney

Contributor · added in 3.3.0

Emmett Sprecher

Contributor

Olink

Copyright holder, Funder

Olof Mansson

Contractor

olofmansson

Releases (25)

Pick two releases to compare their code metrics.

5.1.0Latest
record
2026-09-18 · current release · diff ↗ ·
added 4 exports
extract_check_log, new_olink_class, rm_check_log, update_check_log
5.0.2
record
2026-06-23 · diff ↗
R
R 4.6.0 released · 2026-04-24
5.0.0
record
2026-01-28 · diff ↗ ·
removed 1 export
%>%

added 9 exports
check_npx, clean_npx, olink_bridge_selector, olink_display_plate_dist, olink_display_plate_layout, olink_ordinal_regression, olink_ordinal_regression_posthoc, olink_osi_dist_plot, read_npx
4.5.0
record
2026-01-28 · diff ↗
4.4.0
record
2025-12-02 · diff ↗
4.3.2
record
2025-09-25 · diff ↗
4.3.1
record
2025-08-01 · diff ↗
4.3.0
record
2025-06-24 · diff ↗
R
R 4.5.0 released · 2025-04-11
4.2.0
record
2025-02-24 · diff ↗
4.1.2
record
2025-01-27 · diff ↗ ·
added 1 export
olink_bridgeability_plot
4.0.2
record
2024-11-22 · diff ↗
4.0.1
record
2024-09-24 · diff ↗
3.8.2
record
2024-06-27 · diff ↗ ·
added 1 export
olink_lod
R
R 4.4.0 released · 2024-04-24

Show 15 earlier eventsHide 15 earlier events

3.7.0
record
2024-02-22 · diff ↗
3.6.2
record
2024-01-13 · diff ↗
3.6.0
record
2023-11-03 · diff ↗
3.5.1
record
2023-08-08 · diff ↗
3.4.1
record
2023-05-08 · diff ↗
3.4.0
record
2023-04-26 · diff ↗ ·
added 3 exports
olink_normalization_bridge, olink_normalization_n, olink_normalization_subset
R
R 4.3.0 released · 2023-04-21
3.3.1
record
2023-02-27 · diff ↗
3.3.0
record
2023-01-24 · diff ↗
3.2.2
record
2022-11-16 · diff ↗
3.2.0
record
2022-11-01 · diff ↗ ·
added 1 export
olink_umap_plot
3.1.0
record
2022-06-10 · diff ↗ ·
added 9 exports
olink_heatmap_plot, olink_one_non_parametric, olink_one_non_parametric_posthoc, olink_ordinalRegression, olink_ordinalRegression_posthoc, olink_pathway_enrichment, olink_pathway_heatmap, olink_pathway_visualization, olink_wilcox
R
R 4.2.0 released · 2022-04-22
3.0.0
record
2022-02-10
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-02-10
Total releases: 25 / 4 yrs
License: AGPL (>= 3) OSI · relicensed from GPL-3 in 3.1.0
Minimum R: ≥ 4.1.0
Bundled data: 465 KB / 3 files
Download size: 2.4 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("OlinkAnalyze")

Format

Nevola, K., Olink, Barbagallo, J., Cambronero, C., Caster, O., Chin, K., Conze, L., Diamanti, K., Dong, K., Eriksson, P., Forsberg, S., Guess, J., Hodén, K., Kar, A., Lötstedt, B., Mansson, O., Moloney, N., Pollo, S., Pucholt, P., Sandin, M., Sheikhi, M., Sprecher, E., Topouza, D., & Zhang, B. (2026). OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink (Version 5.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.OlinkAnalyze

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for OlinkAnalyze version 5.1.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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