Single-cell Pipeline
by @aipoch-ai
Generate single-cell RNA-seq analysis code templates for Seurat and Scanpy, supporting QC, clustering, visualization, and downstream analysis. Trigger when u...
Generate Seurat Template
python scripts/main.py --tool seurat --output seurat_analysis.R --species human
Generate Scanpy Template
python scripts/main.py --tool scanpy --output scanpy_analysis.py --species mouse
Generate Both Templates
python scripts/main.py --tool both --output scrna_pipeline --species human --batch-correction harmony --trajectory true
Command-Line Parameters
| Parameter | Type | Required | Description |
|-----------|------|----------|-------------|
| --tool | string | Yes | Analysis tool: seurat, scanpy, or both |
| --output | string | Yes | Output file or directory path |
| --species | string | No | Species: human or mouse (default: human) |
| --batch-correction | string | No | Method: harmony, rpca, cca, scanorama, scvi |
| --trajectory | bool | No | Include trajectory analysis (default: false) |
| --cell-communication | bool | No | Include cell-cell communication (default: false) |
| --de-analysis | bool | No | Include differential expression (default: false) |
| --spatial | bool | No | Include spatial transcriptomics (default: false) |
# Python dependencies
pip install -r requirements.txt
clawhub install single-cell-rnaseq-pipeline