Estimate cell state transitions and trajectory directions from single-cell RNA-seq data.
npx skills add https://github.com/galeep/plugin-place --skill scvelo-galeep
Please help me install this Agent Skill. Skill: scvelo Source: https://github.com/galeep/plugin-place/tree/main/plugins/sci-bioinformatics-genomics/skills/scvelo Command: npx skills add https://github.com/galeep/plugin-place --skill scvelo-galeep
This Skill addresses the need for analyzing RNA velocity in single-cell RNA-seq data to estimate cell state transitions and infer trajectory directions.
Run the RNA velocity analysis on your data using the scVelo skill.
High-intent search queries and answers about installing and using this skill.
RNA velocity analysis estimates cell state transitions and infers trajectory directions in single-cell RNA-seq data by applying dynamical modeling to spliced and unspliced RNA count matrices.
RNA velocity analysis requires an AnnData object containing separate 'spliced' and 'unspliced' count layers, along with pre-computed UMAP annotations to visualize the inferred trajectory directions.
Yes, trajectory inference results integrate with scanpy and matplotlib to visualize cell state transitions and project velocity vectors directly onto existing UMAP embeddings within the single-cell RNA-seq analysis pipeline.
Dynamical modeling works with single-cell RNA-seq count matrices but specifically requires pre-processed spliced and unspliced RNA layers within an AnnData object to calculate RNA velocity and estimate cell state transitions.
RNA velocity analysis is needed when studying developmental processes or dynamic cell state transitions over time, allowing you to identify key cell states and infer trajectory directions from a single snapshot.
Spliced and unspliced RNA layers are necessary because trajectory inference uses the ratio of unspliced to spliced mRNA to calculate transcriptional changes, enabling the estimation of future cell states in single-cell RNA-seq data.
AlterLab-IEUAnalyze RNA velocity to infer cell state transitions from spliced and unspliced counts.
felixboehmPerform RNA velocity analysis on single-cell RNA-seq data with scVelo.
robotlearning123Perform single-cell RNA-seq analysis with scanpy from loading to visualization.
qinyan-aiInfer RNA velocity and latent time from spliced and unspliced mRNA in AnnData objects.
