ClonoDynamics reproducibility dataset: processed TCR repertoires, pseudo-longitudinal technical reference, longitudinal analysis outputs, and synthetic validation

ClonoDynamics is a reproducibility dataset accompanying the ClonoDynamics study on replicate-resolved inference of longitudinal T-cell receptor repertoire dynamics. The archive contains: - exact processed clonotype-level repertoire inputs used by the production pipeline;- frozen pseudo-longitudinal design manifests for 2,000 randomized configurations generated from 12 independent technical measurements;- pair-fit parameters and provenance for the 66 unique unordered technical-measurement pairs;- compact Step 7 and Step 8 pseudo-reference outputs;- the central longitudinal transition dataset and compact outputs from the primary longitudinal analyses and robustness controls;- frozen empirical calibration, oracle definitions, verification outputs, and summary results for the synthetic positive-control workflow;- final manuscript Supplementary Data workbooks (Data 1–Data 11);- reproducibility metadata, software-environment freeze, and SHA256 integrity manifests. Raw FASTQ sequencing data are not duplicated in this archive and are available from the NCBI Sequence Read Archive under BioProject PRJNA1457834 and SRA Study SRP694925. Very large deterministic computational intermediates, including expanded pseudo-transition caches, per-configuration checkpoint files, large posterior/logP matrices, full expanded trajectory tables, and synthetic scenario repertoires, are intentionally omitted because they can be regenerated from the frozen inputs, manifests, random seeds, and software release.