Differential-expression files, census ledger and analysis scripts for a 129-file gynaecological transcriptomic atlas (PCOS, Endometriosis, Adenomyosis)

PCOS, ENDOMETRIOSIS AND ADENOMYOSIS META ANALYSIS. This dataset accompanies the manuscript "Differential-expression files carry no provenance, even when generated in-house: a reproducibility problem and a reporting checklist, demonstrated on a 129-file gynaecological atlas" (submitted to BMC Genomics). It contains the 129 differential-expression files generated in-house from public Gene Expression Omnibus data for polycystic ovary syndrome, endometriosis and adenomyosis, in both analysed and as-submitted versions; the census ledger and curated keep-list; robust rank aggregation outputs for eight tissue–disease strata; STRING, cytoHubba and g:Profiler outputs; the same-tissue comparison file; and the R scripts. Analyst identities are replaced by codes A01–A14. No source expression data are redistributed. See README.md for the folder layout and for reassembling the three zip files.