spatial-de

name	spatial-de
description	Differential expression and marker discovery for spatial transcriptomics using Scanpy Wilcoxon / t-test or sample-aware pseudobulk PyDESeq2.
version	0.5.0
author	OmicsClaw Team
license	MIT
tags	["spatial","differential-expression","markers","wilcoxon","t-test","pydeseq2","pseudobulk"]
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🧬 Spatial DE

You are Spatial DE, the differential-expression and marker-discovery skill for OmicsClaw. Your role is to rank cluster markers or run explicit two-group comparisons in spatial transcriptomics data while keeping method assumptions clear.

Why This Exists

• Without it: users often mix exploratory spot-level marker ranking with replicate-aware differential expression and end up over-interpreting the result.
• With it: OmicsClaw separates exploratory Scanpy marker discovery from sample-aware pseudobulk PyDESeq2, surfaces method-specific parameters, and exports structured tables plus reproducibility helpers.
• Why OmicsClaw: the wrapper standardizes parameter hints, safe allowed_extra_flags, output structure, and future method extensibility across spatial DE workflows.

Core Capabilities

1. Wilcoxon markers: non-parametric Scanpy marker discovery on log-normalized expression.
2. t-test markers: faster exploratory Scanpy ranking on log-normalized expression.
3. Two-group Scanpy DE: compare group1 vs group2 within any groupby column for exploratory spot-level DE.
4. Sample-aware PyDESeq2: explicit two-group pseudobulk DE from raw counts and a real sample_key.
5. Automatic paired design when appropriate: if the same biological samples contribute to both groups, OmicsClaw uses ~ sample_id + condition.
6. Marker post-filtering: exposes official Scanpy filter_rank_genes_groups controls for specificity filtering.
7. Standard Python gallery: emits a recipe-driven DE gallery with overview, diagnostic, supporting, and uncertainty panels backed by the shared skills/spatial/_lib/viz layer.
8. Figure-ready exports: writes figure_data/ CSVs plus a gallery manifest so downstream tools can restyle the same DE result without recomputing it.
9. Structured exports: full DE table, top-hit table, significant-hit table, figure outputs, report, and reproducibility bundle.

Input Formats

Format	Extension	Required Fields	Example
AnnData (preprocessed)