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Atlas of Computational Cell Reprogramming

Indexed methods

This catalog lists peer reviewed computational methods for cell reprogramming. A method is included only if, given a source cell distribution and a target identity or phenotype, it explicitly predicts an intervention designed to move the source toward the target, while upstream tools such as trajectory inference, optimal transport, and landscape reconstruction are enabling methods, they are not included here. The index launched with the 60 methods audited in the companion review and now lists 60, growing as new peer reviewed methods are added. Each entry is classified by explicitness class (C0, C1, C2, C3) and reprogramming setting at publication. Search below or open any entry for placement rationale, reproducibility scores, and links to the primary paper and source code.

Structured filters follow the SI_2 table. Validation (V0 to V4) and uncertainty (U0 to U4) are evidence descriptors, not quality ranks.

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Class
Setting
Intervention

60 indexed methods

Method Publication Year Class Setting Intervention Reproducibility Score FAIR4RS Score Software

Propose a newly published method via /submit. Additions and audit refreshes are logged on the changelog (release v0.2.2).