scientific-spatial-transcriptomics
CommunityEnd-to-end spatial transcriptomics with Squidpy.
Authornahisaho
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Automates end-to-end spatial transcriptomics analysis, enabling preprocessing, detection of spatially variable genes, automatic spatial domain identification, cell-type deconvolution, and ligand-receptor proximity analysis within a Squidpy-aligned workflow.
Core Features & Use Cases
- Preprocessing of spatial data (quality control, normalization) and integration with common spatial libraries.
- Spatial domain discovery and gene pattern detection (Moran's I / SpatialDE / BayesSpace / STAGATE).
- Cell-type deconvolution in spatial spots using reference scRNA-seq datasets (cell2location).
- Spatial ligand-receptor interaction analysis to study inter-domain signaling.
- Use Case: Researchers analyzing Visium or Slide-seq datasets to map tissue architecture and cellular interactions.
Quick Start
Load spatial data, run preprocessing, detect SVG and domains, perform deconvolution, and visualize spatial patterns in Squidpy.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 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: scientific-spatial-transcriptomics Download link: https://github.com/nahisaho/satori/archive/main.zip#scientific-spatial-transcriptomics 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 471,000+ vetted skills library on demand.