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

TL;DR

sCIRCLE is a tool for exploring single-cell RNA-seq data, especially for bacteria, using interactive 2D and 3D visualizations.

Contribution

sCIRCLE introduces an interactive, information design-focused tool for visual exploration of bacterial scRNA-seq data.

Findings

sCIRCLE supports 2D and 3D projections of scRNA-seq data with interactive metadata queries.

The tool includes features like dimensionality reduction, gene filtering, and fold change computation.

It enables real-time visualization and data import/export for standalone use.

Abstract

sCIRCLE (single-Cell Interactive Real-time Computer visualization for Low-dimensional Exploration) is a tool for exploratory analysis of single cell RNA-seq (scRNA-seq) data sets, with a focus on bacterial scRNA-seq. The software takes an information design perspective to re-envision visually and interactively exploring low dimensional representations of scRNA-Seq data. Users can project cells in various 3D and 2D spaces and interactively query and paint cells using rich metadata sets reporting on cell cluster, gene function, and gene expression. As a standalone application it contains, among other features, options for dimensionality reduction, navigation and interaction with data in 3d and 2d space, gene filtering, fold change and metacell computation as well as various capabilities for visualization, data import and export.

Figures