spatial-transcriptomics
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.
Pinned to revision aa24bdca5f23, so it is the text this page describes rather than whatever the author pushed since.
Files
- skills/spatial-transcriptomics/SKILL.md
- skills/spatial-transcriptomics/configs/gold_chain.example.json
- skills/spatial-transcriptomics/configs/platform_configs.yml
- skills/spatial-transcriptomics/scripts/_common.py
- skills/spatial-transcriptomics/scripts/spatial_clustering.py
- skills/spatial-transcriptomics/scripts/spatial_deconvolution.py
- skills/spatial-transcriptomics/scripts/spatial_inspect.py
- skills/spatial-transcriptomics/scripts/spatial_io.py
- skills/spatial-transcriptomics/scripts/spatial_niche_analysis.py
- skills/spatial-transcriptomics/scripts/spatial_pipeline.py
- skills/spatial-transcriptomics/scripts/spatial_plot.py
- skills/spatial-transcriptomics/scripts/spatial_preprocessing.py
- skills/spatial-transcriptomics/scripts/spatial_variable_genes.py
- skills/spatial-transcriptomics/scripts/spatial_visualization.py
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