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tooluniverse-rnaseq-deseq2

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Production-ready RNA-seq differential expression analysis using PyDESeq2. Performs DESeq2 normalization, dispersion estimation, Wald testing, LFC shrinkage, and result filtering. Handles multi-factor designs, multiple contrasts, batch effects, and integrates with gene enrichment (gseapy) and ToolUniverse annotation tools (UniProt, Ensembl, OpenTargets). Supports CSV/TSV/H5AD input formats and any organism. Use when analyzing RNA-seq count matrices, identifying DEGs, performing differential expression with statistical rigor, or answering questions about gene expression changes.

When to use

• Have RNA-seq count matrices and want differential expression analysis
• Ask about DESeq2, DEGs, differential expression, padj, log2FC
• Need dispersion estimates or diagnostics
• Want enrichment analysis (GO, KEGG, Reactome) on DEGs
• Ask about specific gene expression changes between conditions
• Need to compare multiple strains/conditions/treatments
• Ask about batch effect correction in RNA-seq
• Questions mention "count data", "count matrix", "RNA-seq", "transcriptomics"

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