·tooluniverse-spatial-omics-analysis
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tooluniverse-spatial-omics-analysis

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mims-harvard/tooluniverseGitHub: mims-harvard/tooluniverseSource: mims-harvard/tooluniverse

Computational analysis framework for spatial multi-omics data integration. Given spatially variable genes (SVGs), spatial domain annotations, tissue type, and disease context from spatial transcriptomics/proteomics experiments (10x Visium, MERFISH, DBiTplus, SLIDE-seq, etc.), performs comprehensive biological interpretation including pathway enrichment, cell-cell interaction inference, druggable target identification, immune microenvironment characterization, and multi-modal integration. Produces a detailed markdown report with Spatial Omics Integration Score (0-100), domain-by-domain characterization, and validation recommendations. Uses 70+ ToolUniverse tools across 9 analysis phases. Use when users ask about spatial transcriptomics analysis, spatial omics interpretation, tissue heterogeneity, spatial gene expression patterns, tumor microenvironment mapping, tissue zonation, or cell-cell communication from spatial data.

mims-harvard·tooluniverse·spatial·omics·analysis
95Installs·2Trend·@mims-harvard

Installation

GitHub: mims-harvard/tooluniverse
$npx skills add https://github.com/mims-harvard/tooluniverse --skill tooluniverse-spatial-omics-analysis

How to Install tooluniverse-spatial-omics-analysis

Quickly install tooluniverse-spatial-omics-analysis AI skill to your development environment via command line

  1. Open Terminal: Open your terminal or command line tool (Terminal, iTerm, Windows Terminal, etc.)
  2. Run Installation Command: Copy and run this command: npx skills add https://github.com/mims-harvard/tooluniverse --skill tooluniverse-spatial-omics-analysis
  3. Verify Installation: Once installed, the skill will be automatically configured in your AI coding environment and ready to use in Claude Code, Cursor, or OpenClaw

Source: mims-harvard/tooluniverse.

SKILL.md

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Comprehensive biological interpretation of spatial omics data. Transforms spatially variable genes (SVGs), domain annotations, and tissue context into actionable biological insights covering pathway enrichment, cell-cell interactions, druggable targets, immune microenvironment, and multi-modal integration.

| svgs | Yes | Spatially variable genes (gene symbols) | ['EGFR', 'CDH1', 'VIM', 'MYC', 'CD3E'] | | tissuetype | Yes | Tissue/organ type | brain, liver, lung, breast, skin | | technology | No | Spatial omics platform used | 10x Visium, MERFISH, DBiTplus, SLIDE-seq |

| diseasecontext | No | Disease if applicable | breast cancer, Alzheimer disease, liver cirrhosis | | spatialdomains | No | Dict mapping domain name to marker genes | {'Tumor core': ['MYC','EGFR'], 'Stroma': ['VIM','COL1A1']} | | celltypes | No | Cell types identified in deconvolution | ['Epithelial', 'T cell', 'Macrophage', 'Fibroblast'] |

Facts (cite-ready)

Stable fields and commands for AI/search citations.

Install command
npx skills add https://github.com/mims-harvard/tooluniverse --skill tooluniverse-spatial-omics-analysis
Source
mims-harvard/tooluniverse
Category
{}Data Analysis
Verified
✓
First Seen
2026-02-20
Updated
2026-03-10
URL
https://www.learn-skills.dev/en/skills/mims-harvard/tooluniverse/tooluniverse-spatial-omics-analysis

Browse more skills from mims-harvard/tooluniverse

Quick answers

What is tooluniverse-spatial-omics-analysis?

Computational analysis framework for spatial multi-omics data integration. Given spatially variable genes (SVGs), spatial domain annotations, tissue type, and disease context from spatial transcriptomics/proteomics experiments (10x Visium, MERFISH, DBiTplus, SLIDE-seq, etc.), performs comprehensive biological interpretation including pathway enrichment, cell-cell interaction inference, druggable target identification, immune microenvironment characterization, and multi-modal integration. Produces a detailed markdown report with Spatial Omics Integration Score (0-100), domain-by-domain characterization, and validation recommendations. Uses 70+ ToolUniverse tools across 9 analysis phases. Use when users ask about spatial transcriptomics analysis, spatial omics interpretation, tissue heterogeneity, spatial gene expression patterns, tumor microenvironment mapping, tissue zonation, or cell-cell communication from spatial data. Source: mims-harvard/tooluniverse.

How do I install tooluniverse-spatial-omics-analysis?

Open your terminal or command line tool (Terminal, iTerm, Windows Terminal, etc.) Copy and run this command: npx skills add https://github.com/mims-harvard/tooluniverse --skill tooluniverse-spatial-omics-analysis Once installed, the skill will be automatically configured in your AI coding environment and ready to use in Claude Code, Cursor, or OpenClaw

Where is the source repository?

https://github.com/mims-harvard/tooluniverse

Details

Category
{}Data Analysis
Source
skills.sh
First Seen
2026-02-20

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