Skill name
spatial-transcriptomics
What it does
End-to-end spatial transcriptomics pipeline for 10x Genomics Visium data. Loads SpaceRanger output, runs
QC, clustering, and marker gene detection, then computes spatially variable genes (Moran's I),
neighbourhood enrichment, and co-occurrence analysis — all in a single reproducible report.
Bioinformatics tools it wraps
Squidpy, Scanpy, leidenalg
Input / Output
- Input: 10x SpaceRanger
outs/ directory (filtered_feature_bc_matrix/ + spatial/)
- Output: Markdown report with UMAP, spatial scatter plots, marker heatmap, Moran's I table,
neighbourhood enrichment matrix, and reproducibility bundle
Why it matters
Spatial transcriptomics is now mainstream but there is no ClawBio skill for it. Researchers running
Visium experiments currently have to stitch together Squidpy tutorials manually. This skill gives them a
one-command pipeline with a demo mode that requires no input data.
Are you willing to implement it?
Skill name
spatial-transcriptomics
What it does
End-to-end spatial transcriptomics pipeline for 10x Genomics Visium data. Loads SpaceRanger output, runs
QC, clustering, and marker gene detection, then computes spatially variable genes (Moran's I),
neighbourhood enrichment, and co-occurrence analysis — all in a single reproducible report.
Bioinformatics tools it wraps
Squidpy, Scanpy, leidenalg
Input / Output
outs/directory (filtered_feature_bc_matrix/+spatial/)neighbourhood enrichment matrix, and reproducibility bundle
Why it matters
Spatial transcriptomics is now mainstream but there is no ClawBio skill for it. Researchers running
Visium experiments currently have to stitch together Squidpy tutorials manually. This skill gives them a
one-command pipeline with a demo mode that requires no input data.
Are you willing to implement it?