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lobster-bioinformatics
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Run bioinformatics analyses using Lobster AI - single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and visualization. Use when analyzing genomics data, searching for papers/datasets, or working with H5AD, CSV, GEO/SRA accessions, or biological data. Requires lobster-ai package installed.
When to use
- Analyze single-cell RNA-seq data (QC, clustering, annotation, markers)
- Perform bulk RNA-seq analysis (differential expression, complex designs)
- Search scientific literature (PubMed, PMC, full-text retrieval)
- Discover datasets (GEO, SRA, ENA (free) and PRIDE, MASSive (cloud))
- Run quality control on biological data
- Generate bioinformatics visualizations (UMAP, volcano plots, heatmaps)
- Download and process biological datasets
- Work with H5AD, CSV, Excel, 10X formats
When not to use
- Lobster requires active LLM provider (Ollama/Anthropic/Bedrock)
- Large datasets (>100K cells) may be slow depending on system resources
- Some features require premium subscription (proteomics, metadata assistant)
- Full-text paper access limited by journal availability
- Rate limits apply when using cloud LLM providers
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