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Documentation Index

Fetch the complete documentation index at: https://docs.synthesize.bio/llms.txt

Use this file to discover all available pages before exploring further.

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Usage Examples

The best prompts clearly state the two groups you want to compare and, when relevant, the sequencing modality.

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Prompt patterns that work well

Use prompts like these: 
Use Synthesize Bio to compare gene expression between heart and liver cells.

Use the Synthesize Bio connector to analyze lung adenocarcinoma tumor vs normal lung tissue.

Analyze CD4+ T cells vs CD8+ T cells in single-cell RNA-seq mode using Synthesize Bio.

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How to make prompts better

Include the details that matter most:
  • the two groups to compare
  • whether the request is bulk or single-cell
  • the tissue, cell type, disease context, or condition

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Tips

  • Keep the comparison focused on two groups.
  • Use direct comparison language such as A vs B.
  • If you want biological interpretation after the analysis, ask for it in a follow-up prompt.

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Example follow-up prompts

After the analysis is complete, users can continue with questions like: 
Summarize the top up-regulated and down-regulated genes in plain English.

Explain which pathways seem most relevant based on these differentially expressed genes.

Turn the result into a short research-style summary I can share with my team.
If a user runs into issues, continue to Troubleshooting.