VeloSim

VeloSim simulates single-cell RNA sequencing (scRNA-seq) data to model gene-expression kinetics along defined cellular trajectories for benchmarking trajectory inference and RNA velocity estimation methods.

Key Features:

• Trajectory Simulation: Accepts predefined trajectory structures including linear, cycle, and cycle-tree to simulate diverse developmental processes.
• Gene-Expression Kinetics: Simulates mRNA generation dynamics and produces both unspliced and spliced mRNA count matrices.
• RNA Velocity Estimation: Computes true RNA velocity measurements along trajectories to indicate direction and speed of cellular transitions.
• Benchmarking Capability: Generates datasets with varying levels of biological and technical variation for evaluating trajectory inference and RNA velocity methods.
• Output Annotations: Produces cell pseudo-time annotations alongside count matrices and true RNA velocity measurements.

Scientific Applications:

• Developmental Dynamics: Study molecular mechanisms driving cellular dynamics during differentiation and development using simulated scRNA-seq data.
• Method Benchmarking: Benchmark and validate trajectory inference and RNA velocity estimation methods using ground-truth unspliced/spliced matrices, pseudo-time, and true velocities.
• Algorithm Development: Develop and test algorithms for single-cell genomics, including trajectory reconstruction and velocity-based analyses.

Methodology:

Takes predefined trajectory structures (e.g., linear, cycle, cycle-tree) as input and simulates gene-expression kinetics (mRNA generation) along these paths to output unspliced and spliced mRNA count matrices, cell pseudo-time annotations, and true RNA velocity measurements with varying biological and technical variation.