mLLMCelltype: Cell Type Annotation Using Large Language Models

Automated cell type annotation for single-cell RNA sequencing data using consensus predictions from multiple large language models. Integrates with Seurat objects and provides uncertainty quantification for annotations. Supports various LLM providers including OpenAI, Anthropic, and Google. For details see Yang et al. (2025) <doi:10.1101/2025.04.10.647852>.

Version: 2.0.0
Imports: dplyr, httr (≥ 1.4.0), jsonlite (≥ 1.7.0), R6 (≥ 2.5.0), digest (≥ 0.6.25), magrittr, stats, tools, utils
Suggests: knitr, rmarkdown, Seurat
Published: 2026-02-08
DOI: 10.32614/CRAN.package.mLLMCelltype
Author: Chen Yang [aut, cre, cph]
Maintainer: Chen Yang <cafferychen777 at tamu.edu>
BugReports: https://github.com/cafferychen777/mLLMCelltype/issues
License: MIT + file LICENSE
URL: https://cafferyang.com/mLLMCelltype/
NeedsCompilation: no
Citation: mLLMCelltype citation info
Materials: README, NEWS
CRAN checks: mLLMCelltype results

Documentation:

Reference manual: mLLMCelltype.html , mLLMCelltype.pdf
Vignettes: Advanced Features & Case Studies (source, R code)
Consensus Annotation Principles (source, R code)
Contributing Guide (source, R code)
Frequently Asked Questions (source, R code)
Getting Started with mLLMCelltype (source, R code)
Installation Guide (source, R code)
Introduction to mLLMCelltype (source, R code)
mLLMCelltype: Overview and Quick Reference (source, R code)
Usage Tutorial (source, R code)
Version History & Changelog (source, R code)
Consensus vs Single-Agent: A Methodology Comparison (source, R code)
Why Choose Consensus? The Scientific Foundation of Multi-LLM Annotation (source, R code)

Downloads:

Package source: mLLMCelltype_2.0.0.tar.gz
Windows binaries: r-devel: mLLMCelltype_1.3.2.zip, r-release: mLLMCelltype_1.3.2.zip, r-oldrel: not available
macOS binaries: r-release (arm64): mLLMCelltype_1.3.2.tgz, r-oldrel (arm64): mLLMCelltype_1.3.2.tgz, r-release (x86_64): mLLMCelltype_1.3.2.tgz, r-oldrel (x86_64): mLLMCelltype_1.3.2.tgz
Old sources: mLLMCelltype archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=mLLMCelltype to link to this page.