Velocyto

Velocyto estimates RNA velocity from single-cell RNA sequencing (scRNA-seq) data to infer the time derivative of gene expression and predict future cellular states.

Key Features:

• Distinguishes Between Unspliced and Spliced mRNAs: Differentiates unspliced and spliced mRNA molecules to capture nascent versus mature transcript abundances.
• Predicts Future Cellular States: Computes the time derivative of gene expression to infer trajectory directions and predict future cellular states on a timescale of hours.
• High-Dimensional Vector Analysis: Outputs high-dimensional RNA velocity vectors representing transcriptome dynamics for individual cells.

Scientific Applications:

• Developmental Lineage Analysis: Infers developmental lineages and cellular dynamics in contexts such as embryogenesis and tissue regeneration.
• Cross-Platform Validation: Has been validated across multiple published datasets and technical platforms.
• Branching Lineage Trees: Reveals complex branching lineage trees, for example in the developing mouse hippocampus.
• Transcription Kinetics Examination: Enables examination of transcription kinetics in systems such as human embryonic brain development.

Methodology:

Distinguishes unspliced and spliced mRNAs, computes RNA velocity as the time derivative of gene expression, and represents velocities as high-dimensional vectors.