Spatial Gene Panel Design

Overview

Pick exactly N genes that let an imaging-based platform identify every major cell type of a tissue. Code builds the evidence; you (the agent) make the final selection from the evidence table and write a reason per gene. Output: a per-gene evidence table and final_gene_panel.csv with N genes, the cell type each marks, its evidence and a reason.

When to Use

• Designing a custom Xenium, MERFISH or CosMx gene panel for a tissue and state
• Choosing add-on genes to extend a vendor base panel for missing cell types
• Checking that a proposed panel can separate the cell types the study needs
• Documenting why each panel gene was chosen, with reference and database evidence
• Comparing candidate markers from a reference with PanglaoDB and CellMarker 2.0
• Use spatial-transcriptomics-cell-type-annotation instead when the panel already exists and data must be annotated
• For genes the panel will not measure, use the gene imputation route of spatial-mapping-tangram after the experiment