R Observatory: Metrics for SpaTopic version 1.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SpaTopic

1.3.1Package record

Topic Inference to Identify Tissue Architecture in Multiplexed Images

0packages depend

3.1Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Xiyu PengCRAN page ↗GitHub ↗Website ↗Issues ↗

A novel spatial topic model to integrate both cell type and spatial information to identify the complex spatial tissue architecture on multiplexed tissue images without human intervention. The Package implements a collapsed Gibbs sampling algorithm for inference. The method is highly scalable to large-scale image datasets without extracting neighborhood information for every single cell. The package supports spatially resolved cell-level data analysis, topic inference, visualization, and downstream biological interpretation of tissue microenvironments.

Install

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

install.packages("SpaTopic", 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("xiyupeng/SpaTopic")

Development version from xiyupeng/SpaTopic. 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-spatopic

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-SpaTopic

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-SpaTopic

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: 5.9 min · r-release-macos-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-01

Show 6 earlier changesHide 6 earlier changes

ERROR12 OK, 1 ERROR2026-04-28
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-04-10
ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.1

READMEYes · 516 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.3.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 14includes a package overview page
Examples that run: 67%4 run in a plain check · 1 never run · 1 hold no code
Exported functions with examples: 44%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

SpaTopic Basics

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #10,516 · ~8/day · ~258/mo

Releases R versions

Daily download trend is not available in this view yet.

27930 days

99690 days

3.1K1 year

Compare downloads with other packages →

Also on362 r2u

How downloads are counted

Repository

xiyupeng/spatopic ↗Account: xiyupeng

18Stars

3Forks

0Open issues

0Open PRs

4Releases

129Commits

3Commit identities

License file reads as GPL-3.0 · 129 commits · Last activity 2026-06-05 · 0% stars, 30d · Default branch at 1.3.1.9000, ahead of CRAN 1.3.1 (checked 2026-10-25)

Responsiveness

How these are sampled

PRs merged (all time): 75%
Median days to close, 50 most recently updated closed issues: 67
Median days to close, 50 most recently updated closed PRs: 4

Stars over time

2025-08-22 · 112026-07-07 · 18

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/xiyupeng/spatopic on 2026-10-25.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-06-05

Coverage (1)

Coverage reporting

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing SpaTopic adds 14 packages (10 with compiled code, 18 MB of source tarballs). Heaviest: sf 9.3 MB, s2 2.8 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.5.0

Imports (6)

Rcpp RANN sf methods (>= 3.4)foreach iterators

LinkingTo (3)

Rcpp RcppArmadillo RcppProgress

Suggests (5)

knitr rmarkdown SeuratObject doParallel spelling

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)

Xiyu Peng

Author, Maintainer since 1.0.1 (2024)

Nikki Xiao

Author · added in 1.3.1

Releases (4)

Pick two releases to compare their code metrics.

1.3.1Latest
record
2026-05-29 · current release · diff ↗ ·
added 6 exports
frex_topic, label_topics, lift_topic, prob_topic, score_topic, stratified_sampling_3D_via_2D
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.2.0
record
2025-03-03 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1.0
record
2024-04-23 · diff ↗
1.0.1
record
2024-01-17
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-01-17
Total releases: 4 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Bundled data: 487 KB / 1 file
Download size: 433 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("SpaTopic")

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

It points to 10.1038/s41467-025-61821-y.

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 SpaTopic version 1.3.1 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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