GeneScope

The Gene Program Interpreter is a Claude Skill for context-aware interpretation of gene programs from Perturb-seq and single-cell data. Every experiment yields dozens of programs, and today interpreting one takes days of manual literature review — while enrichment tools give generic labels and LLM-only tools sound plausible without being grounded in the specific biological context. GPI injects that context — cell type, tissue, conditions, and, for Perturb-seq, the supporting regulators, perturbation effects, gene weights, and direction — throughout the workflow, so each program is read as a context-specific regulatory response rather than a generic gene list. It combines deterministic database evidence (enrichment, interactions), one Claude Agent SDK literature agent per program searching over MCP, a deterministic verifier that confirms every citation resolves to a real paper, and Anthropic Batch-API annotation — into an auditable, interactive HTML report. Across recent runs it interprets a program for about half a dollar and a few minutes of autonomous research, with every verified citation that you can read directly. Packaging it as a Skill makes the workflow plug-and-play and agent-native. Any scientist could use their Claude to refine context interactively on their own data, and generate publication-ready resource page.

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