R Observatory: Metrics for HDStIM version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HDStIM

0.1.0

High Dimensional Stimulation Immune Mapping ('HDStIM')

0packages depend

2.6Kdownloads / year

81.8%test coverage

9/13checks pass

Overview

About

Maintained by Rohit FarmerFirst published 2022-06-241 releasesCRAN page ↗GitHub ↗

A method for identifying responses to experimental stimulation in mass or flow cytometry that uses high dimensional analysis of measured parameters and can be performed with an end-to-end unsupervised approach. In the context of in vitro stimulation assays where high-parameter cytometry was used to monitor intracellular response markers, using cell populations annotated either through automated clustering or manual gating for a combined set of stimulated and unstimulated samples, 'HDStIM' labels cells as responding or non-responding. The package also provides auxiliary functions to rank intracellular markers based on their contribution to identifying responses and generating diagnostic plots.

Install

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

install.packages("HDStIM", 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("niaid/HDStIM")

Development version from niaid/HDStIM. 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-hdstim

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-HDStIM

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-HDStIM

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

4NOTE9OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64

Slowest check: 6.1 min · r-devel-linux-x86_64-debian-clang

Code health

Yes

Tests · ratio 0.12

81.8%

Coverage · measured lines

100%

Documentation · exports

10

Dependencies · direct

Check history

NOTE2026-05-17
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 197 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 60%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.6K

CRAN downloads in the past year

Rank #17,256 · ~7/day · ~214/mo

Releases R versions

Daily download trend is not available in this view yet.

14430 days

62190 days

2.6K1 year

Compare downloads with other packages →

Also on88 r2u19 autocran

Repository

GitHub ↗ niaid/hdstim

3Stars

0Forks

2Open issues

0Open PRs

0Releases

91Commits

3Contributors

cytometrycytometry-analysis-pipelinecytofflowcytometrystimulationassayr-package

91 commits · Last activity 2023-10-05

Stars over time

2022-10-28 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/niaid/hdstim on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (10)

tibble ggplot2 uwot dplyr tidyr broom tidyselect ggridges Boruta scales

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Rohit Farmer

Author, Maintainer

Authors (3)

Rohit Farmer

Author, Maintainer

Richard Apps

Author

John Tsang

Author, pdr

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2022-06-24
Total releases: 1 / 4 yrs
License: CC0 | file LICENSE
Minimum R: ≥ 3.6.0
Bundled data: 540 KB / 1 file
Download size: 816 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("HDStIM")

Format

Farmer, R., Apps, R., & Tsang, J. (2022). HDStIM: High Dimensional Stimulation Immune Mapping ('HDStIM') (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.HDStIM

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 HDStIM version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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