lobster-transcriptomics
Single-cell and bulk RNA-seq analysis agents for the Lobster AI platform.
Installation
pip install lobster-transcriptomics
Agents
| Agent | Description |
|---|---|
transcriptomics_expert |
Parent orchestrator for single-cell and bulk RNA-seq workflows. Handles QC, clustering, and coordinates sub-agents. |
annotation_expert |
Cell type annotation specialist. Automated and manual annotation, debris detection, annotation templates. |
de_analysis_expert |
Differential expression specialist. Pseudobulk aggregation, pyDESeq2, pathway enrichment. |
Services
| Service | Purpose |
|---|---|
| EnhancedSingleCellService | Single-cell clustering and analysis workflows |
| PseudobulkService | Aggregate single-cell data to pseudobulk for DE analysis |
| DifferentialFormulaService | Formula-based differential expression with pyDESeq2 |
| QualityService | Comprehensive QC metrics calculation and filtering |
| PreprocessingService | Normalization, log transformation, and preprocessing |
| ManualAnnotationService | Manual cluster annotation with template support |
| AnnotationTemplates | Tissue-specific marker gene templates (PBMC, brain, lung) |
| BulkVisualizationService | Publication-quality plots for bulk RNA-seq results |
Features
- Auto-detection of single-cell vs bulk RNA-seq data types
- Comprehensive QC metrics including gene counts, mitochondrial %, and ribosomal %
- Flexible filtering with data-type-appropriate default thresholds
- Leiden clustering with multi-resolution support and quality metrics
- UMAP visualization with automatic point size scaling
- Deviance-based highly variable gene selection
- Batch correction for multi-sample experimental designs
- Sub-clustering for heterogeneous cell populations
- Tissue-specific annotation templates for rapid cell type identification
- Pseudobulk aggregation from single-cell to bulk format
- Formula-based DE analysis supporting complex experimental designs
- GO and KEGG pathway enrichment for biological interpretation
Requirements
- Python 3.12+
- lobster-ai >= 1.0.0
Documentation
Full documentation: docs.omics-os.com/docs/agents/transcriptomics
License
MIT
1 maintainer
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