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bio-spatial-transcriptomics-spatial-domains - Spatial Domain Detection in Transcriptomics Data

Identify spatial domains and tissue regions using expression and spatial clustering methods

Tags

Updated: 2026-03-20
spatial transcriptomicsclusteringbioinformaticsSquidpydomain detection

Capabilities

build spatial neighbor graphrun Leiden clusteringcombine expression and spatial graphsdetect spatial domains

Typical Inputs

spatial transcriptomics dataspatial coordinates

Typical Outputs

spatial domain assignmentsdomain marker genesclustering evaluation scores

What this skill does

  • build spatial neighbor graph
  • run Leiden clustering
  • combine expression and spatial graphs
  • detect spatial domains
  • evaluate clustering quality
  • find marker genes
  • annotate tissue domains

Inputs

  • spatial transcriptomics data
  • spatial coordinates

Outputs

  • spatial domain assignments
  • domain marker genes
  • clustering evaluation scores

Requirements

  • Python environment
  • Squidpy
  • Scanpy

Source

  • Spec: SKILL.md

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