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omicverse-single-cell-rna-velocity

Automate single-cell RNA velocity analysis on AnnData objects with OmicVerse.

13|2|Updated Apr 5, 2026
Search Tags:#single-cell#omicverse#anndata#rna velocity#velocity-backend#graphvelo
One-click install
npx skills add https://github.com/Starlitnightly/omicverse-skills --skill omicverse-single-cell-rna-velocity
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: omicverse-single-cell-rna-velocity
Source: https://github.com/Starlitnightly/omicverse-skills/tree/main/src/omicverse_skills/skills/single-cell-rna-velocity
Command: npx skills add https://github.com/Starlitnightly/omicverse-skills --skill omicverse-single-cell-rna-velocity

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires anndata, omicverse, matplotlib, numpy, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

Automates end-to-end RNA velocity analysis on velocity-ready AnnData objects using OmicVerse, enabling reproducible workflows and easy cross-backend comparisons.

Core Features & Use Cases

  • Unified workflow: preprocessing, velocity estimation, and embedding via ov.single.Velo and related ov.pp helpers.
  • Supports multiple velocity backends (scvelo, dynamo, latentvelo, graphvelo) and GraphVelo refinement for downstream visualization.
  • Real-world use-case: compare backends on the same dataset to identify the most reliable velocity estimates and generate publishable plots.

Quick Start

Load a velocity-ready AnnData and execute the end-to-end velocity workflow through the Velo wrapper to obtain velocities and embeddings.

Frequently Asked Questions about omicverse-single-cell-rna-velocity

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run single-cell RNA velocity analysis on an AnnData object using OmicVerse?▼

Run single-cell RNA velocity on an AnnData object using the OmicVerse ov.single.Velo wrapper to automate preprocessing, velocity estimation, and embedding projection in an end-to-end workflow.

Can I compare scvelo, dynamo, latentvelo, and graphvelo backends on the same dataset?▼

You can compare scvelo, dynamo, latentvelo, and graphvelo velocity backends on the same AnnData dataset using the unified OmicVerse Velo wrapper to identify the most reliable velocity estimates.

What input data format is required for OmicVerse RNA velocity estimation?▼

OmicVerse RNA velocity estimation requires a velocity-ready AnnData object containing either raw velocity counts or distinct spliced and unspliced layers within the data structure.

How does GraphVelo refinement improve single-cell velocity embeddings?▼

GraphVelo refinement improves single-cell velocity embeddings by applying graph-based refinement to raw velocity estimates, generating refined projections like velocity_S_graph and velocity_gv_umap for downstream visualization.

What velocity keys are generated after running the OmicVerse velocity workflow?▼

The OmicVerse velocity workflow generates multiple velocity keys in the AnnData object, including velocity_S, velocity_S_graph, velocity_S_umap, velocity_gv, and velocity_gv_umap for downstream analysis.

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