Spatial transcriptomics tutorials with omicverse
CommunityMaster spatial transcriptomics analysis.
System Documentation
What problem does it solves? Analyzing spatial transcriptomics data involves complex steps from image processing and cell segmentation to deconvolution and advanced spatial modeling, often requiring diverse tools and expertise. This Skill provides a comprehensive guide to these workflows, simplifying the analysis of Visium, Visium HD, Stereo-seq, and Slide-seq datasets.
Core Features & Use Cases
- Spatial Preprocessing: Crop, rotate, and align spatial slides, and perform Visium HD cell segmentation with Cellpose.
- Spatial Deconvolution: Deconvolute cell types using methods like Tangram, cell2location, and Starfysh.
- Downstream Spatial Modeling: Conduct spatial clustering, multi-slice integration, trajectory modeling, and cell communication analysis.
- Use Case: Analyze a Visium HD dataset, segment cells using Cellpose, then deconvolve cell types with cell2location, and finally infer spatial communication networks between identified cell populations.
Quick Start
Preprocess my Visium HD data, segment cells with Cellpose, then run Tangram deconvolution, and visualize the inferred cell-type proportions.
Dependency Matrix
Required Modules
Components
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: Spatial transcriptomics tutorials with omicverse Download link: https://github.com/Starlitnightly/omicverse/archive/main.zip#spatial-transcriptomics-tutorials-with-omicverse Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
Agent Skills Search Helper
Install a tiny helper to your Agent, search and equip skill from 223,000+ vetted skills library on demand.