Analysis archive for "Reference choice governs apparent cortical-organoid fidelity in cross-study genomic contrasts"

Analysis archive for "Reference choice governs apparent cortical-organoidfidelity in cross-study genomic contrasts". Contains the compact derived effect tables, dataset and cohort manifests,SHA-256 checksum ledger, figure source data and figure-generation code,frozen preregistrations and configuration, seeds, and computationalexecution records. No manuscript text is included; the manuscript ispublished separately. This version extends v1 with the age-ordered reference series: sixdevelopmental anchors fitted from a single atlas, region and sequencingchemistry, with the exact-permutation trend test, the adjacent-stepdecomposition, and the leave-one-reference-donor-out refits. Analyses were produced with RefGauge v0.2.0 (10.5281/zenodo.21794556),built from commit 5db6b33a199ac3bf73c97cb9564bf6224446c75a. Derived and descriptive artifacts only. No participant-level raw human dataare redistributed; primary sources are cited by accession and remain intheir original repositories under those repositories' terms. Absolute machine paths in the frozen audit records are replaced by portabletokens; see README.md in the archive.