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.

Use Spatial transcriptomics gold chain (squidpy) in Claude, ChatGPT or Ahel Desktop

Free. Sign in, add Spatial transcriptomics gold chain (squidpy) and connect your AI. About a minute.

Claude ChatGPT Ahel Desktop

Also: Claude Code · Cursor · Codex

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

Details

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.

No other account needed.

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

Spatial transcriptomics gold chain (squidpy)Start free

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

Advanced

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

github.com/herry423/bionexus

Spatial transcriptomics gold chain (squidpy)

Use Spatial transcriptomics gold chain (squidpy) in Claude, ChatGPT or Ahel Desktop

What this skill tells your AI

Signals

Related picks