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de-results

separate

Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing correction choice (BH vs Storey q-value vs IHW vs lfsr), TREAT vs post-hoc fold-change filtering, p-value histogram diagnostics, gene annotation via org.db/biomaRt/mygene, GSEA preranked input, ORA background construction, replication reality (Schurch 2016 small-n result), and SABV/sex-stratified reporting. Use when extracting and interpreting DE results, troubleshooting padj=NA, choosing FDR method, preparing ranked lists for pathway analysis, annotating gene IDs, or comparing DESeq2 vs edgeR outputs.

When to use

• extracting and interpreting DE results
• troubleshooting padj=NA
• choosing FDR method
• preparing ranked lists for pathway analysis
• annotating gene IDs
• comparing DESeq2 vs edgeR outputs
• handling independent filtering and Cook's outliers
• SABV/sex-stratified reporting

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