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Cell type markers for annotation and discovery

Fast, reliable and automatic cell type annotation using the largest manually curated database of cell type signatures
CellKb Interface CellKb Results CellKb Analysis
๐ŸŽ‰ CELEBRATING 5 YEARS ๐ŸŽ‰
Thank you for being part of our journey

Cell type markers for annotation and discovery

Fast, reliable and automatic cell type annotation using the largest manually curated database of cell type signatures
๐ŸŽ‰ CELEBRATING 5 YEARS ๐ŸŽ‰
Thank you for being part of our journey

Cell type markers for
annotation and discovery

Fast, reliable and automatic cell type annotation using the largest manually curated database of cell type signatures
CellKb Knowledgebase
The largest manually curated reference database of cell type signatures
128,571
Signatures
1,724
Cell Types
1,824
Publications
3,065
Tissues
1,000
Diseases
13
Species
CellKb v2.11 Updated: 1st Aug 2025   (Release notes)
What Scientists Say
Trusted by leading researchers in academia and industry
CellKb has been transformative for our work in so many unexpected ways beyond its powerful single-cell RNA-seq interface and tools. From predicting cell types from bulk transcriptomics measurement to annotating hundreds of thousands of spots from spatial transcriptomics and more, its high accuracy, high quality database has become a central piece of our bioinformatics infrastructure.
Associate Professor, University of Chicago
I routinely use CellKb for annotating my single-cell RNA-seq datasets, and I must say, it exceeds my expectations in every way. CellKb streamlined the entire process with its comprehensive, literature-backed, reference database, and intuitive interface. As a Core lab working across many biological systems, CellKbโ€™s powerful annotation capabilities allow us to confidently annotate single cell data sets without having to become experts in the biology of the organism or tissue.
Director, Bioinformatics Core, Salk Institute
Our lab has been using CellKb since 2020 for annotating cell types in single-cell and spatial transcriptomics data. CellKb is powered by a highly curated database derived from a large number of studies leading to significantly low batch-to-batch variability, which we struggled with in the past when using small data sets as reference. CellKb is supported by an expert team of bioinformaticians at Combinatics who are always willing to help and clarify doubts within 24 hours.
Associate Professor, University of South Australia
CellKb Functionality
Use our in-built reference database and marker based method for fast, accurate and automatic cell type annotations
Cluster annotation

Predict cell types for cluster-specific gene lists.

Single-cell annotation

Annotate individual cells in scRNA-seq datasets.

Spatial deconvolution

Assign cell types in spatial RNA-seq datasets.

Bulk cell type enrichment

Find cell type abundance in bulk RNA-seq data.

Consensus signatures

View consensus signatures for cell types in disease.

Biomarker discovery

Get top marker genes for cell types in tissues.

Why use CellKb?
Our literature-backed marker gene list based solution to cell type annotation sets us apart from other methods
High-quality in-built reference

Large number of cell types, tissues, diseases and species available in a single, curated resource.

Marker based annotation

Fast rank-based matching method compares upregulated genes with every cell type signature from all references independently.

Granular cell type predictions

Get broad and granular predicted cell types with publications and previously used canonical markers for confirmation.

AI-ready annotations

Standardized ontologies for cell types, tissues and diseases for AI-ready data labeling.

Search across organisms

Annotate cell types in non-model organisms using reference data from model organisms.

Regular updates

Our database is updated with the latest publications every 4 months.

Our Community
3300+ Users
600+ Organizations
Trusted by leading organizations worldwide
Alnylam
Benevolent AI
Johnson & Johnson
Merck Group
Baylor College of Medicine
IBS, South Korea
University of Tokyo
University of Toronto