spatial-transcriptomicslisted
Orchestrator skill for spatial transcriptomics analysis. Routes to one of three personality modes (aristotle/plato/socrates) based on user intent. Covers platforms: Visium, Xenium, MERFISH, Slide-seq, Stereo-seq, CosMx, SpatialDB, Seq-Scope, DBiT-seq, STARmap. Frameworks: Scanpy, Squidpy, Giotto, Seurat, SpatialDE, BayesSpace, SPARK-X, SpaGCN, Cell2location, RCTD, Tangram. Trigger keywords: spatial transcriptomics, Visium, Xenium, MERFISH, Slide-seq, spatial gene expression, spatial omics, single-cell spatial, spatial analysis, spot deconvolution, spatial clustering, spatially variable genes, 空间转录组, 空间组学, 空间基因表达, 空间分析, 空间聚类, 空间差异表达, 10x Visium, Stereo-seq, CosMx, seqFISH, FISSEQ.
Nigmat-future/TopoLogos · ★ 0 · API & Backend · score 72
Install: claude install-skill Nigmat-future/TopoLogos
# Spatial Transcriptomics — Mode Router
## Decision Tree
Route user requests to one of three personality modes. Detect intent from keywords in
the user's natural language question, then load the corresponding mode file.
```
User Question
│
├── Contains Socrates markers?
│ "全新" "颠覆" "换思路" "unconventional" "breakthrough"
│ "rethink" "from scratch" "无预设" "paradigm shift"
│ "abandon standard" "completely new direction"
│ → YES → Load modes/socrates.md
│
├── Contains Plato markers?
│ "新方法" "前沿" "cutting-edge" "recent" "improved"
│ "最新" "更好的方法" "state of the art" "alternative"
│ "compare methods" "beyond standard" "最新进展"
│ → YES → Load modes/plato.md
│
├── Contains Aristotle markers?
│ "标准流程" "常规分析" "standard pipeline" "routine analysis"
│ "best practice" "tried and tested" "gold standard"
│ "recommended workflow" "standard preprocessing" "QC"
│ → YES → Load modes/aristotle.md
│
└── No clear markers (DEFAULT)
→ Load modes/aristotle.md (safety-first)
```
**Ambiguity resolution**: When markers from multiple modes are present, use this priority:
`socrates > plato > aristotle`. Novelty-seeking overrides safety defaults. If only
"novel" appears without stronger markers, route to plato mode.
## Mode Overview
### Aristotle (`modes/aristotle.md`)
Standard, reproducible spatial transcriptomics pipelines using well-established tools
(Scanpy, Squidpy, Seurat).