R Observatory: Metrics for stIHC version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

stIHC

0.1.1Package record

Spatial Transcriptomics Iterative Hierarchical Clustering

0packages depend

1.6Kdownloads / year

74.7%test coverage

13/13flavors OK

Overview

About

Maintained by Catherine HigginsCRAN page ↗

Spatial transcriptomics iterative hierarchical clustering ('stIHC'), is a method for identifying spatial gene co-expression modules, defined as groups of genes with shared spatial expression patterns. The method is applicable across spatial transcriptomics technologies with differing spatial resolution, and provides a framework for investigating the spatial organisation of gene expression in tissues. For further details, see Higgins C., Li J.J., Carey M. doi:10.1002/qub2.70011.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)

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

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

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-stihc

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-stIHC

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

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 12.5 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-05

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-03-29
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 1
Examples that run: 0%1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

stIHC-introduction HTML

How these are measured

Downloads

1.6K

CRAN downloads in the past year

Rank #23,743 · ~5/day · ~137/mo

Releases R versions

Daily download trend is not available in this view yet.

22530 days

53390 days

1.6K1 year

Compare downloads with other packages →

Also on52 r2u

How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing stIHC adds 34 packages (20 with compiled code, 32 MB of source tarballs). Heaviest: bslib 5.6 MB, rgl 4.0 MB, sass 2.9 MB.

Depends (1)

R >= 4.0.0

Imports (4)

fdaPDEstatsclustermclust

LinkingTo (0)

none

Suggests (4)

testthat knitr rmarkdown covr

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 (3)

Catherine Higgins

Author, Maintainer since 0.1.0 (2026)

Michelle Carey

Author

Jingyi Jessica Li

Author

Releases (2)

Pick two releases to compare their code metrics.

0.1.1Latest
record
2026-10-21 · current release · diff ↗ ·
17 hours in CRAN's queue
Listed in CRAN's incoming queue from 2026-10-20 17:40 to 2026-10-21 10:55 UTC, in 5 readings.
R
R 4.6.0 released · 2026-04-24
0.1.0
record
2026-01-12
R
R 4.5.0 released · 2025-04-11

Across CRAN, the median accepted release of the past year spent 23 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2026-01-12
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Download size: 182 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("stIHC")

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

It points to 10.1002/qub2.70011.

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 stIHC version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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