CloneImmuneCo: Reproducible Analysis Code, Derived Data, Provenance, and Figures for Clonotype-Associated CD8 T-Cell Transcription

This record provides the reproducible analysis archive for the manuscript “Clonotype-associated CD8 T-cell transcription replicates across independent cohorts without establishing antigen reactivity.” The archive contains pinned Python analysis code, public-data download and verification workflows, frozen model metadata, automated tests, machine-readable derived results, robustness analyses, provenance records, checksums, and final main and supplemental figures. The study analyzes paired single-cell RNA and T cell receptor (RNA/TCR) sequencing data across independent human CD8 T-cell cohorts to evaluate the reproducibility of clonotype-associated transcription and to define the limits of inferring antigen reactivity from that signal. Raw participant-level public files, processed H5AD objects, cached third-party repositories, and superseded analysis outputs are not redistributed. Public source accessions, repository versions and commits, available checksums, software dependencies, and reproduction instructions are documented within the archive. This release corresponds to version 1.0.0 of the analysis package.