SlimR

1.1.7

Adaptive Machine Learning-Powered, Context-Matching Tool for Single-Cell and Spatial Transcriptomics Annotation

0packages depend

4.6Kdownloads / year

26.3%test coverage

13/13checks pass

Overview

About

Maintained by Zhaoqing WangFirst published 2025-07-2911 releasesCRAN page ↗GitHub ↗

Annotates single-cell and spatial-transcriptomic (ST) data using context-matching marker datasets. It creates a unified marker list (`Markers_list`) from multiple sources: built-in curated databases ('Cellmarker2', 'PanglaoDB', 'ScType', 'scIBD', 'TCellSI', 'PCTIT', 'PCTAM'), Seurat objects with cell labels, or user-provided Excel tables. SlimR first uses adaptive machine learning for parameter optimization, and then offers two automated annotation approaches: 'cluster-based' and 'per-cell'. Cluster-based annotation assigns one label per cluster, expression-based probability calculation, and AUC validation. Per-cell annotation assigns labels to individual cells using three scoring methods with adaptive thresholds and ratio-based confidence filtering, plus optional UMAP spatial smoothing, making it ideal for heterogeneous clusters and rare cell types. The package also supports semi-automated workflows with heatmaps, feature plots, and combined visualizations for manual annotation. For more information, see the package documentation at https://github.com/zhaoqing-wang/SlimR.

Install

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

install.packages("SlimR", 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("zhaoqing-wang/SlimR")

Development version from zhaoqing-wang/SlimR. 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-slimr

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-SlimR

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-SlimR

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

Health

CRAN checks

13OK

Slowest check: 10.9 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.19

26.3%

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
OK2026-04-10
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 · 1,333 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 13%
Documented parameters: 100%
Return-value docs: 100%
References docs: 2%

Downloads

4.6K

CRAN downloads in the past year

Rank #6,478 · ~13/day · ~384/mo

Releases R versions

Daily download trend is not available in this view yet.

34230 days

1.5K90 days

4.6K1 year

Compare downloads with other packages →

Also on206 r2u14 autocran

Repository

GitHub ↗ zhaoqing-wang/slimr

7Stars

2Forks

1Open issues

0Open PRs

17Releases

324Commits

1Contributors

324 commits · Last activity 2026-07-27 · +16.7% stars, 30d

Stars over time

2025-07-27 · 12026-07-11 · 7

Repository practices

Upstream repositoryBeta

Checks run against github.com/zhaoqing-wang/slimr on 2026-07-26.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (12)

cowplot dplyr ggplot2 patchwork pheatmap readxl scales Seurat tidyrtoolstibble gtools

LinkingTo (0)

none

Suggests (4)

crayon RANN testthat WeightedTreemaps

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Zhaoqing Wang

Author, Maintainer · added in 1.0.8

Authors (1)

Zhaoqing Wang

Author, Maintainer · added in 1.0.8

Listed in earlier versions (1)

Zhao qing Wang

no longer listed · 1.0.3 to 1.0.7

Package Timeline

11 releases. Pick two to compare their code metrics. R releases are shown for context.

1.1.7Latest
2026-07-22 · current release · diff ↗
1.1.6
2026-06-30 · diff ↗
1.1.5
2026-06-03 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.1.3
2026-04-07 · diff ↗
1.1.2
2026-03-13 · diff ↗
1.1.1
2026-02-05 · diff ↗
1.1.0
2026-01-20 · diff ↗
1.0.9
2025-12-17 · diff ↗
1.0.8
2025-10-08 · diff ↗
1.0.7
2025-08-19 · diff ↗
1.0.3
2025-07-29
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-07-29
Total releases: 11 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 2.6 MB / 13 files
Download size: 2.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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