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Process ScVelo Specifications

Process Details

  • Name: Process ScVelo
  • Process UUID: 99ac31fb94ab458bb6aaf5bf3270e229
  • Process Group: SingleCell

Overview

This process performs RNA velocity analysis using scVelo to infer cell state transitions and developmental trajectories in single-cell RNA sequencing data. It computes velocity vectors, transition probabilities, and macrostate fate probabilities to understand cellular dynamics and predict future cell states based on spliced and unspliced mRNA counts.

This process is implemented in Bash, which invokes a Python script for velocity analysis using the scVelo framework.

Key Functionality

  • RNA Velocity Computation: Calculates velocity vectors from spliced and unspliced mRNA counts to predict future cell states
  • Transition Probability Analysis: Computes transition probabilities between cell states using configurable K-step predictions
  • Macrostate Identification: Identifies coarse-grained cell states and calculates fate probabilities for trajectory analysis
  • Cluster-Specific Analysis: Allows selective analysis of specific cell clusters or comprehensive analysis of all clusters

Input/Output Specification

Inputs

Required Inputs

  • Single Cell Data
    • Description: Annotated single-cell data containing spliced and unspliced mRNA counts with cluster annotations
    • Format: h5ad

Outputs

  • Velocity Analysis Results
    • Description: Single-cell data enhanced with velocity vectors, transition probabilities, and macrostate annotations
    • Format: h5ad

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Condition Column

    • Description: Name of condition column
    • Default value: Condition

  • Number of K Steps

    • Description: Number of K steps to compute transition probabilities. Higher K = longer-term predictions.
    • Default value: 1,2,3

  • Number of Macrostates

    • Description: Number of course-grained cell states for fate probability analysis. High values = more detailed trajectory structure.
    • Default value: 10

  • Target Clusters

    • Description: Select specific clusters to include in analysis. Leave empty to analyse all clusters.
    • Default value: (empty - analyzes all clusters)

References & Resources

  • Tool Documentation: Contact the team for details on precompute_analysis.py
  • Related Papers: Bergen, V., Lange, M., Peidli, S. et al. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat Biotechnol 38, 1408–1414 (2020). https://doi.org/10.1038/s41587-020-0591-3