The Auditable Modular Expression Laboratory (AMEL): an integrated R/Shiny platform for reproducible bulk RNA-seq analysis and interpretation

AMEL (Auditable Modular Expression Laboratory) is a modular Shiny application packaged as an R package for downstream bulk RNA-seq analysis. From a raw count matrix and sample metadata it provides differential expression (DESeq2), quality-control diagnostics, sample overviews (PCA / UMAP / 3D PCA), a linked volcano-table explorer, multi-contrast comparison, functional enrichment (GSEA / ORA), co-expression network analysis (WGCNA), transcription-factor and pathway activity inference (decoupleR), per-sample gene-set signatures (GSVA / ssGSEA), optional AI-assisted interpretation, and reproducible R script and self-contained HTML report generation.