^s CIRCLE-An interactive visual exploration tool for single cell RNA-Seq data.

Area of Science:

• Bioinformatics
• Computational Biology
• Data Visualization

Background:

• Single-cell RNA sequencing (scRNA-seq) generates large, complex datasets.
• Exploratory data analysis is crucial for understanding cellular heterogeneity.
• Existing tools may lack interactive and intuitive visualization capabilities for scRNA-seq.

Purpose of the Study:

• To introduce CIRCLE (single-Cell Interactive Real-time Computer visualization for Low-dimensional Exploration), a novel software tool.
• To provide an interactive and visually-driven approach for exploring low-dimensional representations of scRNA-seq data.
• To specifically address the analysis needs of bacterial scRNA-seq datasets.

Main Methods:

• CIRCLE employs an information design perspective for enhanced data exploration.
• The software enables users to project cells into 3D and 2D spaces.
• Interactive querying and 'painting' of cells using metadata (clusters, gene function, expression) are supported.

Main Results:

• CIRCLE facilitates interactive exploration of scRNA-seq data through dynamic visualizations.
• The tool supports dimensionality reduction, navigation, and data interaction in 3D and 2D.
• Features include gene filtering, fold change, and metacell computation for comprehensive analysis.

Conclusions:

• CIRCLE enhances the exploratory analysis of scRNA-seq data, particularly for bacterial applications.
• The interactive visualization approach aids in uncovering patterns and insights within complex datasets.
• The software provides a versatile platform for scRNA-seq data visualization, import, and export.