Model RNA velocity from spliced and unspliced counts in AnnData.
npx skills add https://github.com/SciMate-AI/scicli --skill scvelo-scimate-ai
Please help me install this Agent Skill. Skill: scvelo Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/scvelo Command: npx skills add https://github.com/SciMate-AI/scicli --skill scvelo-scimate-ai
RNA velocity analysis with scVelo enables inference of dynamic cell states from static single-cell RNA-seq data by modeling spliced and unspliced mRNA dynamics to reveal directionality of cell-state transitions.
Load an AnnData object with spliced and unspliced layers, then run the scvelo velocity workflow to estimate RNA velocity and latent time.
High-intent search queries and answers about installing and using this skill.
RNA velocity is calculated by modeling spliced and unspliced mRNA dynamics from single-cell RNA sequencing data to infer the directionality of cell-state transitions. This requires an AnnData object containing distinct 'spliced' and 'unspliced' count layers.
Estimating latent time and identifying driver genes involves fitting stochastic or dynamical RNA velocity models to spliced and unspliced counts. This approach highlights regulatory dynamics across developmental or differentiation trajectories.
Yes, scVelo integrates seamlessly with Scanpy. You must preprocess your single-cell RNA-seq data using Scanpy to prepare the AnnData object before fitting the velocity models to infer dynamic cell states.
RNA velocity analysis requires spliced and unspliced counts because the mechanism models the transcriptional dynamics between these two mRNA states. By measuring the ratio of unspliced to spliced mRNA, the model infers whether a gene is being induced or repressed.
Yes, scVelo supports dynamical modeling for trajectory inference across developmental or differentiation studies. It fits a dynamical model to spliced and unspliced counts to estimate latent time and recover regulatory dynamics.
RNA velocity for trajectory inference is not suitable when your single-cell dataset lacks spliced and unspliced mRNA count layers. Without these specific layers in your AnnData object, the underlying stochastic or dynamical models cannot be fitted.
dralkhAnalyze RNA velocity data from single-cell transcriptomic matrices with scVelo.
RamanEbrahimiEstimate RNA velocity and cell state transitions from single-cell RNA-seq data.
LeonChaoXInfer RNA velocity and latent time from spliced and unspliced mRNA in AnnData.
Estrella-231Infer RNA velocity and cell fate trajectories from single-cell RNA-seq AnnData.
