RhinitisAtlas: a unified public-transcriptome resource for allergic rhinitis - analysis archive v2

Analysis archive for RhinitisAtlas, a census-complete, uniformly re-analysed public-transcriptome resource for allergic rhinitis (GEO data cutoff 1 October 2026). Contents: (1) curation_table_v3.csv - all 69 GEO series adjudicated at sample level (core 39 / pending 1 / excluded 29) with reasons; (2) results_step3_bulk.zip - per-cohort differential-expression tables (31 contrasts), gene-by-contrast evidence matrices (disease layer and challenge/treatment layer), consensus gene table, sample phenotype tables and run log; (3) results_step4_scrna.zip and results_step4_pseudobulk.zip - single-cell QC reports, donor-level compositions, pseudobulk count matrices and 81 cell-type pseudobulk contrast tables for six datasets (292,545 cells); (4) objects__GSE*_annotated_slim.h5ad - annotated single-cell objects (sparse counts, unified cell-type labels, UMAP coordinates; slimmed from the analysis objects by sparse conversion and gzip, values unchanged), with matching per-cell metadata CSVs; (5) results_step2_step7_docs.zip - curation evidence, step reports and the Step-7 validation battery (marker direction recovery, allergen-challenge induction, immunotherapy-reversal test, abstract-claim reproduction audit); (6) build_scripts.zip - the pipeline code; (7) website_data.zip - the precomputed JSON served by https://yuye8848.github.io/rhinitisatlas/. Raw GEO data are not redistributed; every series is cited by accession in the curation table. FILES_MANIFEST.csv lists every file and the bundle that contains it.Version 2 (2026-11-03) correction: curation v4 fixes the tissue class of GSE118243 (nasal brushing, not blood cells); tissue-stratified analyses were recomputed on the unified 15-contrast nasal stratum and the nasal meta-analysis was rebuilt on fit-derived standard errors. See correction_note_v4.md and correction_v4__results.zip inside the record.