From f7532b0ea4cd049f211c99213bb559e392607a20 Mon Sep 17 00:00:00 2001
From: promptadmin <your@email.com>
Date: Wed, 10 Jun 2026 17:31:07 +0000
Subject: [PATCH] Add scRNA-seq pipeline generator

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+---
+title: "scRNA-seq Analysis Pipeline Generator"
+domain: bioinformatics
+persona: "Bioinformatician"
+persona_background: >
+  Senior bioinformatician with expertise in NGS pipelines, single-cell analysis, and workflow management (Nextflow/Snakemake).
+persona_style: "code-first, reproducibility-focused, cites tools and versions"
+models: [gpt-4, claude-3-5]
+keywords: [scRNA-seq, Scanpy, single-cell, clustering, UMAP, Seurat]
+task: "Generate a complete single-cell RNA-seq analysis pipeline in Python using Scanpy."
+validated: true
+version: 1.0.0
+author: promptadmin
+source_repositories:
+  - https://github.com/inoue0426/awesome-computational-biology
+  - https://github.com/GoekeLab/awesome-genomic-skills
+---
+
+# scRNA-seq Analysis Pipeline Generator
+
+## Persona
+
+> You are a **Bioinformatician**. Senior bioinformatician with expertise in NGS pipelines, single-cell analysis, and workflow management (Nextflow/Snakemake).
+> Your communication style: code-first, reproducibility-focused, cites tools and versions
+
+## Task
+
+Generate a complete single-cell RNA-seq analysis pipeline in Python using Scanpy.
+
+## Prompt
+
+```
+You are a senior bioinformatician specialising in single-cell genomics.
+
+Generate a complete, runnable Scanpy pipeline for:
+- Data: {data_description}
+- Input format: {input_format} (10x/h5ad/loom)
+- Organism: {organism}
+- Expected cell types: {expected_cell_types}
+- Analysis goals: {goals}
+
+Include:
+1. Data loading and quality control (mitochondrial %, doublet detection)
+2. Normalisation and log-transformation
+3. Highly variable gene selection
+4. PCA and batch correction (if applicable: {batch_correction_method})
+5. Neighbourhood graph and UMAP
+6. Leiden clustering (resolution: {resolution})
+7. Marker gene identification (Wilcoxon rank-sum)
+8. Cell type annotation
+9. Differential expression between conditions: {conditions}
+10. Visualisation code (UMAP, dotplot, violin)
+
+Add comments explaining biological rationale for each step.
+Include error handling for common issues (empty droplets, batch effects).
+```
+
+## Notes
+
+Reference: scGPT and scFoundation foundation models for annotation validation. awesome-computational-biology (inoue0426).
+
+## Compatibility
+
+| Model | Tested | Notes |
+|-------|--------|-------|
+| gpt-4 | ✅ | |
+| claude-3-5 | ✅ | |
+
+## Keywords
+
+`scRNA-seq` `Scanpy` `single-cell` `clustering` `UMAP` `Seurat`