CytoAnalyst

Powerful, Flexible & Interactive
Single-Cell RNASeq Analysis Platform

CytoAnalyst is a comprehensive platform for single-cell transcriptomic analysis, offering a wide range of modules and visualization tools. It empowers researchers to explore and analyze complex single-cell data with ease and flexibility.

If our platform contributes to your research, please cite the following publication:

Phi Bya, Duy Tran, Khoi Nguyen, Sorin Draghici, and Tin Nguyen. “CytoAnalyst web platform facilitates comprehensive single cell RNA sequencing analysis.” Scientific Reports 15, no. 1 (2025): 28736.

Advanced & Flexible Visualization

Interactive Grid-Layout Visualization

Visualize your data in a grid layout with interactive and customizable settings.

Visualize multiple labels at once for a more comprehensive view of single-cell data.

Comprehensive Analysis Modules

Quality Control

Validate and ensure reliability of your single-cell RNA-seq data with robust QC metrics and filtering.

Embedding Analysis & Data Integration

Generate and compare multiple embeddings using standard algorithms. Easily integrate datasets for comprehensive analysis.

Clustering

Identify cell populations with multiple clustering methods. Compare results across parameters to validate cell type discovery.

Differential Expression

Identify marker genes between cell populations using multiple statistical methods. Compare results across parameters for robust discoveries.

Gene Set Collection Management

Create, import, and manage gene set collections with our intuitive interface. Access 2,000+ built-in cell type gene sets for immediate analysis.

Cell Enrichment Analysis

Perform gene set enrichment analysis at cell or group level to identify enriched pathways and functional categories in your data.

Cell Annotation & Cell Type Prediction

Annotate cell types using enrichment results or pre-trained neural networks. Leverage LLM support for sophisticated annotation workflows.

And more...

Get ready for more exciting features and modules in the future!

Case Studies

Visit our case studies to see how CytoAnalyst can be applied to real-world datasets. Explore the analysis and visualization capabilities of CytoAnalyst in action.

Clustering & Cell Type Annotations

Performing Clustering and Cell Type Annotation on a Bone Marrow Organoids dataset.

CytoAnalyst

Powerful, Flexible & Interactive
Single-Cell RNASeq Analysis Platform

Advanced & Flexible Visualization

Synchronized Plot Interaction

Interactive Grid-Layout Visualization

Multi Plot Type Visualization

Synchronized Plot Interaction

Interactive Grid-Layout Visualization

Multi Plot Type Visualization

Synchronized Plot Interaction

Comprehensive Analysis Modules

Quality Control

Embedding Analysis & Data Integration

Clustering

Differential Expression

Gene Set Collection Management

Cell Enrichment Analysis

Cell Annotation & Cell Type Prediction

And more...

Case Studies

Differential Expression Analysis

Clustering & Cell Type Annotations

Differential Expression Analysis

Clustering & Cell Type Annotations

Differential Expression Analysis

Powerful, Flexible & InteractiveSingle-Cell RNASeq Analysis Platform

Advanced & Flexible Visualization

Interactive Grid-Layout Visualization

Comprehensive Analysis Modules

Quality Control

Embedding Analysis & Data Integration

Clustering

Differential Expression

Gene Set Collection Management

Cell Enrichment Analysis

Cell Annotation & Cell Type Prediction

And more...

Case Studies

Clustering & Cell Type Annotations

Powerful, Flexible & Interactive
Single-Cell RNASeq Analysis Platform