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- Initial Bioconductor submission.
- Module 1: Data ingestion from GEO/SRA and local files with 10-point QC scoring.
- Module 2: Normalization (TMM, VST, CPM, TPM, quantile) and batch correction (ComBat-seq, ComBat, limma, harmony).
- Module 3: Per-study differential expression via DESeq2, edgeR, and limma-voom.
- Module 4: Meta-analysis statistics — Fisher, Stouffer, inverse-normal, fixed effects, random effects (DerSimonian-Laird), and AWmeta.
- Module 5: Missing gene handling with imputation and coverage filtering.
- Module 6: Pathway meta-analysis using KEGG, Reactome, GO, and MSigDB Hallmarks.
- Module 7: Publication-ready visualization (volcano, forest, heatmap, UpSet plots).
- Module 8: Reproducible HTML/PDF report generation and result export.
