skills.rest
TianGzlab
TianGzlabOFFICIAL
Explore all skills by this author →
GitHub

spatial-trajectory

Infer single-cell trajectories and pseudotime from AnnData or Loom files.

155|26|Updated Mar 14, 2026
Search Tags:#bioinformatics#pseudotime#single-cell#cell differentiation#rna velocity#trajectory inference
One-click install
npx skills add https://github.com/TianGzlab/OmicsClaw --skill spatial-trajectory
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: spatial-trajectory
Source: https://github.com/TianGzlab/OmicsClaw/tree/main/skills/singlecell/sc-trajectory
Command: npx skills add https://github.com/TianGzlab/OmicsClaw --skill spatial-trajectory

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires scanpy, scvelo, rpy2, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the complex process of understanding cellular differentiation and developmental trajectories from single-cell RNA sequencing data, transforming raw data into clear biological insights.

Core Features & Use Cases

  • Trajectory Inference: Utilizes multiple state-of-the-art algorithms (DPT, PAGA, Monocle3, Slingshot) to model cell lineage.
  • RNA Velocity Analysis: Predicts future cell states and differentiation dynamics using scVelo.
  • Pseudotime Ordering: Assigns a developmental time to each cell along inferred trajectories.
  • Use Case: Analyze a dataset of developing immune cells to identify distinct differentiation paths, predict progenitor cell populations, and visualize the flow of cells towards mature states.

Quick Start

Infer cellular trajectories and pseudotime using the DPT method on the provided AnnData file.

Frequently Asked Questions about spatial-trajectory

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

FAQPage Schema
How do I perform single-cell trajectory inference and pseudotime analysis on AnnData files?▼

Single-cell trajectory inference and pseudotime analysis models cellular differentiation dynamics by processing AnnData files using algorithms like DPT, PAGA, and Slingshot to assign developmental time to each cell.

Can I use scVelo for RNA velocity analysis on a Loom file?▼

RNA velocity analysis on a Loom file is supported using scVelo to predict future cell states and differentiation dynamics, allowing you to visualize the flow of cells towards mature states.

Do I need rpy2 installed to run Monocle3 and Slingshot for cell lineage modeling?▼

You need rpy2 installed to run R-based algorithms like Monocle3 and Slingshot for cell lineage modeling, while Python packages like scanpy and scvelo handle other trajectory inference methods directly.

What is the best way to identify progenitor cell populations in developing immune cells?▼

Identifying progenitor cell populations in developing immune cells is best achieved by combining PAGA for abstract lineage graph reconstruction with pseudotime ordering to map distinct differentiation paths.

Does this trajectory inference approach support branching lineage analysis?▼

Trajectory inference supports branching lineage analysis by utilizing state-of-the-art algorithms like DPT and PAGA to model complex cell fate decisions and reveal distinct developmental trajectories.

Why use DPT over PAGA for modeling cellular differentiation dynamics?▼

DPT models cellular differentiation dynamics by measuring diffusion distances between cells to establish pseudotime ordering, whereas PAGA provides an abstract graph of branching lineage topologies at the population level.

Related Skills

Explore More Data & Analytics Skills→
Lord1EgyptLord1Egypt
2

scanpy

Perform end-to-end single-cell RNA-seq analysis with AnnData.

Community
Advanced
StarlitnightlyStarlitnightly
32

cellfate-pseudotime-gene-analysis

Identify lineage-specific fate genes along pseudotime trajectories in scRNA-seq data.

Community
Advanced
Hung-3008Hung-3008
1

scvelo

Model spliced and unspliced mRNA dynamics to identify cell-state transitions in scRNA-seq data.

Community
Advanced
StarlitnightlyStarlitnightly
13

omicverse-single-cell-trajectory-inference

Infer trajectories and summarize lineages on cluster-ready AnnData objects.

Community
Intermediate