spatial-transcriptomics-analysis

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Details

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What this skill tells your AI

The instructions your AI receives, as published by freedomintelligence/openclaw-medical-skills in skills/spatial-transcriptomics-analysis/SKILL.md and read by Ahel’s review.

name: spatial-transcriptomics-analysis description: Automated analysis pipeline for Spatial Transcriptomics (Visium, Xenium) integrating histology and gene expression. keywords:

spatial-transcriptomics
visium
xenium
scanpy
squidpy measurable_outcome: Process a Visium dataset, identify spatially variable genes, and generate spatial feature plots within 30 minutes. license: MIT metadata: author: MD BABU MIA, PhD version: "1.0.0" compatibility:
system: python 3.9+ allowed-tools:
run_shell_command
read_file
write_file

Spatial Transcriptomics Skill

Version: 1.0.0 Author: MD BABU MIA, PhD Date: February 2026

Overview

This skill provides automated analysis capabilities for Spatial Transcriptomics data, specifically designed for 10x Visium and Xenium platforms. It enables the integration of histological data with gene expression profiles to uncover spatial organization of cell types.

Capabilities

Data Loading: Supports Spaceranger output (h5, images).
QC & Preprocessing: Spatial QC metrics, normalization.
Spatial Variable Features: Identification of spatially variable genes (SVGs) using Moran's I and Geary's C.
Deconvolution: Interface for cell type deconvolution (mapping scRNA-seq to spatial).
Visualization: Interactive spatial plots overlaying gene expression on tissue images.

Usage

from Skills.Genomics.Spatial_Transcriptomics.spatial_analyzer import SpatialAnalyzer

# Initialize
sa = SpatialAnalyzer(data_path="./data/visium_sample1")

# Run Pipeline
sa.load_data()
sa.preprocess()
sa.find_spatial_features()
sa.plot_spatial("INS", save_path="./output/insulin_spatial.png")

Requirements

scanpy
squidpy
anndata
matplotlib

Signals

GitHub stars: 3k
Forks: 412
Last commit: Jul 2026

Advanced

Item type: skill
Key: spatial-transcriptomics-analysis
Source: github.com/freedomintelligence/openclaw-medical-skills

github.com/freedomintelligence/openclaw-medical-skills