lobster-transcriptomics 1.0.11

Transcriptomics agents for Lobster AI - single-cell and bulk RNA-seq analysis

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