Data and code archive for "Autophagy-related prognostic signatures report gene expression, not autophagic flux: 169 coded reports from a census of 212"

This archive accompanies the Letter to the Editor named above. It holds the search output, the sentence-level coding, and the scripts that generate every count reported in Table 1 and in the text, so that each figure can be recomputed rather than taken on trust. 212 records were eligible; full text was available for 180; 169 were coded. Reports were placed in three tiers: no autophagy marker measured at the protein or ultrastructural level; marker measured but without a lysosomal inhibitor or tandem reporter, so direction cannot be inferred; and flux-discriminating. Each report was coded twice, once requiring the marker and the method to share a sentence (strict) and once requiring only that they occur in the same document (permissive). The flux tier is identical under both rules, which is why the Letter's conclusion does not depend on how strictly the text was read. https://github.com/lmxch00/Autophagy https://doi.org/10.17605/OSF.IO/9SRG3