CellCraft: an extensible visual programming application for gene regulatory network inference.

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Here, we introduce CellCraft, a web-based application designed to streamline GRN inference. CellCraft integrates multiple GRN reconstruction tools, including TENET, within a unified web application featuring an intuitive graphical user interface. Notably, CellCraft provides a visual programming interface that simplifies the design and execution of complex multistep analyses, thereby enhancing accessibility and facilitating the visualization and interpretation of computational experiments. Furthermore, its modular plugin architecture ensures extensibility, enabling the incorporation of newly developed single-cell analysis algorithms. Consequently, CellCraft provides a user-friendly and extensible application for integrative GRN analysis of scRNA-seq datasets.\nAVAILABILITY AND IMPLEMENTATION: CellCraft is available on GitHub at https://github.com/cxinsys/cellcraft. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["CellCraft is openly accessible at https://cellcraft.app. The source code underlying this article is available on GitHub at https://github.com/cxinsys/cellcraft and archived in Zenodo at https://doi.org/10.5281/zenodo.17865848."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:41452748"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:08:56Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 6064, "completion_tokens": 956, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:41452748", "type": "paper", "label": "pmid:41452748"}, {"id": "source:pmid:41452748", "type": "manuscript", "label": "PMID 41452748 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41452748", "type": "paper", "label": "pmid:41452748"}, {"id": "source:pmid:41452748", "type": "manuscript", "label": "PMID 41452748 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41452748", "type": "extraction", "used": ["source:pmid:41452748"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": null, "parent_hash": null, "fork_of": null, "generation": 0}, "gaps": ["execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ructing gene regulatory networks (GRNs) from single-cell RNA sequencing (scRNA-seq) data is fundamental for understa", "orks (GRNs) from single-cell RNA sequencing (scRNA-seq) data is fundamental for understanding cellu", "application for integrative GRN analysis of scRNA-seq datasets. 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