Cell Journey

Cell Journey enables interactive three-dimensional analysis and visualization of RNA velocity trajectories derived from single-cell datasets.

Key Features:

• 3D RNA Velocity Visualization: Computes RNA velocity vector fields on a user-defined three-dimensional grid and constructs velocity trajectories using either Euler integration or the fourth-order Runge-Kutta method.
• Multimodal Data Support: Supports both unimodal and multimodal single-cell data inputs.
• Multiple Input Formats: Accommodates multiple input formats for single-cell datasets.
• Interactive Visual Elements: Enables dynamic exploration of cellular dynamics through streamlines, streamlets, cones, and volumetric plots.
• Feature Activity Investigation: Allows investigation of changes in feature activity along selected paths to facilitate insights into cellular state transitions.

Scientific Applications:

• Single-Cell Trajectory Analysis: Reconstructs and visualizes dynamic cellular differentiation trajectories at high resolution from single-cell profiling data integrated with RNA velocity analysis.
• Complex Multipartite Transition Analysis: Captures complex topologies of multipartite cellular transitions that are insufficiently represented by two-dimensional visualization techniques.
• Cellular State Transition Investigation: Facilitates deeper insights into cellular state transitions within complex multimodal single-cell datasets through path-specific feature activity analysis.

Methodology:

Cell Journey computes RNA velocity vector fields on a user-defined three-dimensional grid and constructs velocity trajectories using either Euler integration or the fourth-order Runge-Kutta method.