SCI Skills

EN Index
Data & ReproScientific VisualizationFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction
SP

spatial-communication

Maintainer FreedomIntelligence · Last updated April 1, 2026

spatial-communication.

OpenClawNanoClawAnalysisWritingspatial-communicationopenclaw medical skillsadditional scientific toolsspatial

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/spatial-communication

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Analyze ligand-receptor interactions and cell-cell communication in spatial data.
  • adata = sc.read_h5ad('clustered_spatial.h5ad').

Source Doc

Excerpt From SKILL.md

Build spatial neighbors if not already done

sq.gr.spatial_neighbors(adata, coord_type='generic', n_neighs=6)

Run ligand-receptor analysis

sq.gr.ligrec( adata, cluster_key='cell_type', # Column with cell type annotations n_perms=100, # Permutations for significance testing threshold=0.01, # P-value threshold copy=False, )

Get results dictionary

ligrec_results = adata.uns['cell_type_ligrec']

Use cases

  • Use spatial-communication to prepare publication-quality figures.
  • Apply spatial-communication when results need clear visual communication.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • spatial-neighbors - Build spatial graphs (prerequisite)
  • spatial-domains - Identify cell types for communication analysis
  • pathway-analysis - Enrich communication genes for pathways
  • single-cell/markers-annotation - Annotate cell types

Related skills

Related skills

Back to directory
BI
Data & ReproScientific Visualization

bio-chipseq-visualization

Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal a…

OpenClawNanoClawAnalysis
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & ReproScientific Visualization

bio-consensus-sequences

Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific refer…

OpenClawNanoClawAnalysis
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & ReproScientific Visualization

bio-copy-number-cnv-visualization

Visualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or oth…

OpenClawNanoClawAnalysis
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & ReproScientific Visualization

bio-data-visualization-circos-plots

Circular genome visualization with Circos or pycirclize.

OpenClawNanoClawAnalysis
FreedomIntelligence/OpenClaw-Medical-SkillsView