CellFate-Rx Gen-1: frozen model and reproducibility artifacts, version 1.0.2

Abstract

Archived reproducibility bundle for CellFate-Rx Generation 1: a preregistered reanalysis of the six-condition clonal-tracing dataset GEO GSE279162 (generated and deposited by Schaff et al., doi:10.1016/j.xgen.2026.101191). No new data were generated. Tests whether pretreatment transcriptional state carries condition-specific information about future clonal detection, beyond condition identity and captured pretreatment clone abundance, under clone-held-out evaluation, with the ranking test frozen by digest before any ranking statistic was computed. The archive contains the frozen model artifact, the derived clone pseudobulk cache needed to re-run the permutation null, all out-of-fold predictions, the 1,000 per-draw permutation values and 2,000 bootstrap replicates, every stage protocol and record including failed and negative results, the environment lock, and three verification tools that refuse on any modified artifact. A SHA256SUMS manifest accompanies the bundle. Licensing. Software and the frozen model are source-available under the PolyForm Noncommercial License 1.0.0: free for academic, educational, nonprofit and other noncommercial use with no permission request. Any commercial use, including developing or evaluating a commercial product or service before it has earned any revenue, requires a separate license (see COMMERCIAL-LICENSING.md); where that notice and the licence differ, the licence governs. Manuscript text and figures are CC BY 4.0. Third-party datasets retain their original terms.