Awesome scRNA Cell Type Annotation

A comprehensive, curated collection of state-of-the-art single-cell RNA sequencing (scRNA-seq) cell type annotation tools, methods, databases, and resources for bioinformatics researchers and computational biologists.

Cell type annotation is a critical step in single-cell RNA sequencing analysis that involves assigning biological identities to clusters of cells based on their gene expression profiles. This repository serves as a central hub for high-quality tools and resources that can help researchers accurately identify cell types in their scRNA-seq datasets.

This collection only includes high-quality tools that either:

• Have more than 100 stars on GitHub, OR
• Are published in prestigious journals (Cell, Nature, Science and their sister journals, or Genome Biology)

Contents

• Cell Type Annotation Tools
  • Machine Learning Based
  • Reference Based
  • Marker Gene Based
  • Large Language Model Based
• Benchmark Studies
• Databases
  • Cell Marker Databases
  • Reference Datasets
• Tutorials and Workflows
• Community Resources
• Contributing
• Star History
• License

Cell Type Annotation Tools

Tool	Description	Publication	GitHub Stars	Journal
mLLMCelltype	An iterative multi-LLM consensus framework for accurate cell type annotation in single-cell RNA-seq data	Yang C, et al. (2025). Large Language Model Consensus Substantially Improves the Cell Type Annotation Accuracy for scRNA-seq Data.		bioRxiv
GPTCelltype	Automatic cell type annotation with GPT-4 in single-cell RNA-seq analysis	Hou W, Ji Z. (2024). Reference-free and cost-effective automated cell type annotation with GPT-4 in single-cell RNA-seq analysis.		Nature Methods
Seurat	R toolkit for single cell genomics	Satija R, et al. (2015). Spatial reconstruction of single-cell gene expression data.		Nature Biotechnology
SCANPY	Single-Cell Analysis in Python	Wolf FA, et al. (2018). SCANPY: large-scale single-cell gene expression data analysis.		Genome Biology
Celltypist	A tool for semi-automatic cell type classification based on logistic regression	Domínguez Conde C, et al. (2022). Cross-tissue immune cell analysis reveals tissue-specific features in humans.		Science
ScType	Fully-automated and ultra-fast cell-type identification using specific marker combinations	Ianevski A, et al. (2022). Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data.		Nature Communications
scCATCH	Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data	Shao X, et al. (2020). scCATCH: Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data.		iScience
CellAssign	Automated, probabilistic assignment of cell types in scRNA-seq data	Zhang AW, et al. (2019). Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling.		Nature Methods
scArches	Reference mapping for single-cell genomics with cell type transfer	Lotfollahi M, et al. (2021). Mapping single-cell data to reference atlases by transfer learning.		Nature Biotechnology
scGate	Marker-based purification of cell types from single-cell RNA-seq datasets	Andreatta M, et al. (2022). scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets.		Bioinformatics
popV	Ensemble method using popular vote of various cell-type transfer tools	Ergen C, Xing G, et al. (2024). Consensus prediction of cell type labels in single-cell data with popV.		Nature Genetics
Garnett	Cell type classification using marker genes and scRNA-seq data	Pliner HA, et al. (2019). Supervised classification enables rapid annotation of cell atlases.		Nature Methods
scmap	A tool for unsupervised projection of single cell RNA-seq data	Kiselev VY, et al. (2018). scmap: projection of single-cell RNA-seq data across data sets.		Nature Methods
SingleR	Reference-based single-cell RNA-seq annotation	Aran D, et al. (2019). Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage.		Nature Immunology
Azimuth	Reference-based annotation for single-cell data	Hao Y, et al. (2021). Integrated analysis of multimodal single-cell data.		Cell
scBERT	Large-scale pretrained deep language model for cell type annotation	Yang F, et al. (2022). scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data.		Nature Machine Intelligence
scGPT	Foundation model for single-cell multi-omics using generative AI	Cui H, Wang C, et al. (2024). scGPT: toward building a foundation model for single-cell multi-omics using generative AI.		Nature Methods
scDeepSort	Pre-trained cell-type annotation method using deep learning with a weighted graph neural network	Shao X, et al. (2021). scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network.		Nucleic Acids Research
scJoint	Transfer learning for data integration of atlas-scale single-cell RNA-seq and ATAC-seq data	Lin Y, et al. (2022). scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning.		Nature Biotechnology

Benchmark Studies

Study	Description	Publication	Journal
Single-cell RNA-seq annotation benchmarking	Systematic comparison of single-cell RNA-seq cell type annotation methods	Abdelaal et al., 2019	Nature Methods
A comparison of automatic cell identification methods	Benchmarking automatic cell identification methods for scRNA-seq	Zhao et al., 2020	Genome Biology

Databases

Database	Description	Publication	URL
CellMarker	Database of cell markers in different tissues	Zhang et al., 2019	Link
PanglaoDB	Single-cell RNA sequencing database for expression data	Franzén et al., 2019	Link
Cell Ontology	Structured vocabulary for cell types	Diehl et al., 2016	Link

Tutorials and Workflows

Title	Description	URL
Orchestrating Single-Cell Analysis with Bioconductor	Comprehensive guide to scRNA-seq analysis	Link
Seurat - Guided Clustering Tutorial	Tutorial for cell type identification with Seurat	Link

Community Resources

Resource	Description	URL
Single Cell Genomics Day	Annual event dedicated to single-cell genomics	Link
Single Cell Omics	Reddit community for single-cell omics discussions	Link
Bioconductor Single Cell	Collection of Bioconductor packages for single-cell analysis	Link

Contributing

We welcome contributions to this repository! Please read our contributing guidelines before submitting a pull request.

If you find this resource useful, please consider giving it a ⭐️ star to help others discover it!

Star History

License

This repository is licensed under the MIT License - see the LICENSE file for details.

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Keywords: single-cell RNA sequencing, scRNA-seq, cell type annotation, bioinformatics, computational biology, marker genes, reference mapping, machine learning, large language models, cell atlas, cell ontology