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spatial-omics

Analyze spatial transcriptomics and proteomics data using graph-based spatial statistics on AnnData inputs.

29|3|Updated Jun 11, 2026
Search Tags:#bioinformatics#deconvolution#spatial#spatialdata#transcriptomics#squidpy
One-click install
npx skills add https://github.com/inflexa-ai/inflexa --skill spatial-omics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: spatial-omics
Source: https://github.com/inflexa-ai/inflexa/tree/main/skills/spatial-omics
Command: npx skills add https://github.com/inflexa-ai/inflexa --skill spatial-omics

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This skill addresses the complexity of analyzing high-dimensional spatial omics data by providing a structured, reproducible framework for technology-specific workflows, spatial statistics, and domain identification.

Core Features & Use Cases

  • Technology-Specific Guidance: Provides tailored analysis paths for Visium, MERFISH, Xenium, and other spatial platforms.
  • Spatial Statistics: Implements graph-based neighbor analysis, neighborhood enrichment, and spatial autocorrelation (Moran's I/Geary's C).
  • Deconvolution: Supports Bayesian cell type deconvolution using user-supplied scRNA-seq references.

Quick Start

Use the spatial-omics skill to build a spatial neighbor graph and calculate Moran's I for all genes in my AnnData object.

Frequently Asked Questions about spatial-omics

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

FAQPage Schema
How do I calculate spatial autocorrelation for my spatial transcriptomics data?▼

Yes, the skill supports spatial transcriptomics analysis for diverse platforms including Visium, MERFISH, and Xenium, providing tailored analysis paths and standardized graph-based spatial statistics for each technology.

What is the best way to perform cell type deconvolution on spatial omics data?▼

To perform cell type deconvolution on spatial omics data, this skill applies a Bayesian approach using user-supplied scRNA-seq references to estimate the cellular composition of tissue spots, integrating tissue morphology with gene expression profiles.

Do I need an AnnData object to run spatial statistics and neighborhood enrichment?▼

Yes, you need an AnnData-based input to run spatial statistics and neighborhood enrichment, and your data must pass strict spatial coordinate system validation to ensure biological accuracy before graph-based analysis.

Can I use Squidpy and SpatialData frameworks to identify tissue domains in spatial proteomics?▼

You can use Squidpy-compatible, graph-based spatial statistics to identify tissue domains in spatial proteomics by integrating tissue morphology with gene expression profiles, supporting standardized domain identification workflows.

Why does my spatial transcriptomics analysis fail coordinate validation during neighbor graph building?▼

Spatial transcriptomics analysis fails coordinate validation when the AnnData input lacks strict spatial coordinate system adherence, preventing the accurate integration of tissue morphology with gene expression profiles required for graph-based statistics.

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