Reproducibility archive: Version drift in R/Bioconductor RNA-seq workflows (four datasets x four Bioconductor releases)

Sixteen experimental units (four public RNA-seq datasets x four consecutive Bioconductor releases: 3.20 with R 4.4.3, 3.21 with R 4.5.1, 3.22 with R 4.5.1 and 3.23 with R 4.6.1), each an independent execution of one identical downstream pipeline (differential expression, over-representation analysis, gene set enrichment analysis). The archive contains, per unit, the pipeline and results directories with a file-size/checksum manifest and a sessionInfo snapshot; the source-attribution factorial experiment with its crossing outputs, run logs and library inventory; the analysis, verification and figure scripts; the derived tables on which the article's numbers rest; the intermediate reports, including the equidistance check of the Bioconductor 3.21 release; and the figure sets. The four source datasets are public and are not redistributed; they are identified in the article by GEO accession (GSE85331, GSE269445, GSE135251, GSE62000). The binary package libraries that implement the factorial crossing are public Bioconductor builds and are not redistributed either; their exact package versions are recorded in the archive.