Authors
Zeng, Z., Wang, X., Luo, Z., Zheng, Y., Hu, L., Xing, C., Du, H.
Abstract
Advances in bulk, single-cell and spatial omics have transformed biological discovery, yet analysis remains fragmented across packages with incompatible interfaces, heterogeneous dependencies and limited workflow reproducibility. Here, we present OmicClaw, an executable natural-language framework for multi-omics analysis built on the unified OmicVerse ecosystem and the J.A.R.V.I.S. runtime. OmicVerse organizes upstream processing, preprocessing, single-cell, spatial, bulk-transcriptomic and foundation-model workflows into a shared AnnData-centered interface spanning more than 100 methods. J.A.R.V.I.S. converts this ecosystem into a bounded analytical action space by exposing more than 200 registered functions and classes through a registry-grounded, state-aware and recoverable execution layer that validates prerequisites, preserves provenance and supports iterative repair. Rather than relying on unconstrained code generation, OmicClaw translates user requests into traceable workflows over live omics objects. Across a benchmark of 15 tasks spanning scRNA-seq, spatial transcriptomics, RNA velocity, scATAC-seq, CITE-seq and multiome analysis, ov.Agent improved rubric-based performance over bare one-shot large language model baselines, particularly for long-horizon multi-step workflows. OmicClaw further supports external agent access through an MCP-compatible server and a beginner-friendly web platform for interactive analysis, code execution and million-scale visualization. Together, OmicClaw provides a practical foundation for reproducible human AI collaboration in modern multi-omics research. OmicClaw is ready to use at https://github.com/Starlitnightly/omicverse
Preprint server:
bioRxiv
The authors list and abstract were imported from bioRxiv on 18 Mar 2026.
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