Spatial transcriptomics gold chain (squidpy)

SkillDocs & knowledge

squidpy spatial gold chain on SpatialData .zarr or AnnData .h5ad with obsm['spatial']. Use when the user has Visium/Slide-seq/generic spots or cells with coordinates. Builds a knn spatial graph, Moran SVGs, and spatial_scatter plots. Multi-table SpatialData requires --table. Does not run Cell2location, BayesSpace, SpaGCN, or vendor HD/Xenium pipelines. Numeric clusters only.

Instructions available. Your AI can read the instructions. Execution depends on the setup they require.

Account requirements not reviewed. Check the skill instructions before use; ahel provides instructions and does not run this skill.

Add ahel to your AI once: Claude, ChatGPT, Cursor, Claude Code or Codex. Then ask it to use this.

Then ask your AI: use the Spatial transcriptomics gold chain (squidpy) skill

What this skill tells your AI

The instructions your AI receives, as published by herry423/bionexus in skills/spatial-transcriptomics/SKILL.md and read by ahel’s review.

Default path is squidpy, not the legacy fused-graph / NNLS helpers.

python scripts/doctor.py   # need ready.spatial_ready
python skills/spatial-transcriptomics/scripts/spatial_inspect.py visium.h5ad
python skills/spatial-transcriptomics/scripts/spatial_pipeline.py visium.h5ad -o spatial_out.h5ad
python skills/spatial-transcriptomics/scripts/spatial_plot.py spatial_out.h5ad -o figures/ --color leiden
# SpatialData with several tables:
python skills/spatial-transcriptomics/scripts/spatial_inspect.py data.zarr --table table_name

Accepts SpatialData .zarr (requires spatialdata) or .h5ad with obsm['spatial']. Multiple tables refuse unless --table is set.

Step	Script	Backend
inspect	`spatial_inspect.py`	AnnData / SpatialData I/O
pipeline	`spatial_pipeline.py`	`spatial_neighbors_knn` + Moran
deconvolve	`spatial_deconvolution.py`	Tangram optimal transport (`tangram-sc` / PyTorch)
plot	`spatial_plot.py`	`squidpy.pl.spatial_scatter` → `spatial_{color}.png`

Refuses if squidpy is missing for Moran's I. For deconvolution, Tangram deep learning is used with transparent NNLS fallback.

Signals

GitHub stars: 31
Forks: 4
Last commit: Sep 2026

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Item type: skill
Key: spatial-transcriptomics-herry423
Source: github.com/herry423/bionexus

github.com/herry423/bionexus

Spatial transcriptomics gold chain (squidpy)

What this skill tells your AI

Signals

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