stIHC

0.1.0

Spatial Transcriptomics Iterative Hierarchical Clustering

0packages depend

1.1Kdownloads / year

74.7%test coverage

13/13checks pass

Overview

About

Maintained by Catherine HigginsFirst published 2026-01-121 releasesCRAN 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.

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

Slowest check: 9.7 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.08

74.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-05
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-29
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

1.1K

CRAN downloads in the past year

Rank #23,363 · ~3/day · ~92/mo

Releases R versions

Daily download trend is not available in this view yet.

16730 days

47290 days

1.1K1 year

Compare downloads with other packages →

Also on35 r2u

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

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.

Code & Tests

Code Composition

R 346 (84%)Rd 34 (8%)Vignettes 34 (8%)

Code characteristics

Cyclomatic complexity: 4.5 median / 23 max
Test cases: 1 / 0.08 per code line

Test coverage

Line coverage

75%

Expression

76.8%

Tests / Examples

74.7% / 0% ex

Functions

4 1 exported

Complexity

8.5 avg / 23 max

Call network

4 nodes / 3 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

4 functions

Function	Cyclo	Coverage
IHC	23	60%
stIHC exp	5	100%
funIHC	4	100%
silhouette_score	2	100%

People & History

People (3)

Maintainer (1)

Catherine Higgins

Author, Maintainer

Authors (3)

Catherine Higgins

Author, Maintainer

Michelle Carey

Author

Jingyi Jessica Li

Author

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: 2026-01-12
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Download size: 182 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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