R Observatory: Metrics for CytoProfile version 0.2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CytoProfile

0.2.4Package record

Cytokine Profiling Analysis Tool

0packages depend

4.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Shubh SaraswatCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides comprehensive cytokine profiling analysis through quality control using biologically meaningful cutoffs on raw cytokine measurements and by testing for distributional symmetry to recommend appropriate transformations. Offers exploratory data analysis with summary statistics, enhanced boxplots, and barplots, along with univariate and multivariate analytical capabilities for in-depth cytokine profiling such as Principal Component Analysis based on Andrzej Maćkiewicz and Waldemar Ratajczak (1993) doi:10.1016/0098-3004(93)90090-R, Sparse Partial Least Squares Discriminant Analysis based on Lê Cao K-A, Boitard S, and Besse P (2011) doi:10.1186/1471-2105-12-253, Random Forest based on Breiman, L. (2001) doi:10.1023/A:1010933404324, and Extreme Gradient Boosting based on Tianqi Chen and Carlos Guestrin (2016) doi:10.1145/2939672.2939785.

Changes in 0.2.4

Major Changes

New functions 'cyt_univariate' for t-test and wilcoxon rank sum test and 'cyt_univariate_multi' for ANOVA and Kruskal-Wallis test have been added to conduct univariate statistical analysis for multiple groups.
Changed 'cyt_bp' to adapt grouping similar to 'cyt_bp2' so there is no longer a need for separate functions
New function 'cyt_violin' for creating violin plots with statistical comparisons between groups.
Two new helper functions to apply different types of transformations and adjust p-values.
Added more options for scale/transformations in all functions that require it and added p-value adjustment options where needed.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("CytoProfile", 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("saraswatsh/CytoProfile")

Development version from saraswatsh/CytoProfile. 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-cytoprofile

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 7.6 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02

Show 2 earlier changesHide 2 earlier changes

ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.4

READMEYes · 201 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.2.4Citation fileYes · software entry onlyWebsiteYes · pkgdown

Help pages: 26 (1 internal)includes a package overview page
Examples that run: 96%22 run in a plain check · 1 hold no code
Exported functions with examples: 90%
Documented parameters: 96%
Return-value docs: 95%
Help pages citing references: 27%

Vignettes (1)

Getting Started with CytoProfile HTML

How these are measured

Downloads

4.1K

CRAN downloads in the past year

Rank #10,079 · ~11/day · ~345/mo

Releases R versions

Daily download trend is not available in this view yet.

36830 days

1K90 days

4.1K1 year

Compare downloads with other packages →

Also on121 r2u

How downloads are counted

Repository

saraswatsh/cytoprofile ↗Account: saraswatsh

0Stars

0Forks

0Open issues

0Open PRs

6Releases

131Commits

1Commit identities

License file reads as GPL-2.0 · 131 commits · Last activity 2026-02-27

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 3

Releases over time

2025-09-04 · 42026-07-07 · 6

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/saraswatsh/cytoprofile on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Code of conduct

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-02-27 · The repository has a site deploy workflow

pkgdown site last built 2026-02-27

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Installing CytoProfile adds 71 packages (38 with compiled code, 53 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 4.3

Imports (16)

mixOmics dplyr tidyr pROC plot3D caret xgboost randomForest pheatmap e1071 ggplot2 ggrepel gridExtra reshape2 lifecycle data.table

LinkingTo (0)

none

Suggests (8)

spelling BiocManager Ckmeans.1d.dp prodlim testthat knitr rmarkdown devtools

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Shubh Saraswat

Xiaohua Douglas Zhang

Author

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.2.4Latest
record
2026-02-27 · current release · diff ↗ ·
added 6 exports
adjust_p, apply_scale, cyt_export, cyt_univariate, cyt_univariate_multi, cyt_violin
0.2.3
record
2025-12-06 · diff ↗
0.2.2
record
2025-09-04 · diff ↗ ·
added 1 export
cyt_mint_splsda
0.2.1
record
2025-05-19 · diff ↗
0.2.0
record
2025-04-11 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.2
record
2025-04-03
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-04-03
Total releases: 6 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.3
Bundled data: 40 KB / 5 files
Download size: 940 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("CytoProfile")

The package provides a citation file, so citation() returns the authors' own entry.

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 CytoProfile version 0.2.4 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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