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rnaseq-deseq2

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ToolUniverse workflow — Rnaseq Deseq2

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---
name: tooluniverse-rnaseq-deseq2
description: 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.
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# RNA-seq Differential Expression Analysis (DESeq2)

Comprehensive differential expression analysis of RNA-seq count data using PyDESeq2, with integrated enrichment analysis (gseapy) and gene annotation via ToolUniverse.

**BixBench Coverage**: Validated on 53 BixBench questions across 15 computational biology projects covering RNA-seq, miRNA-seq, and differential expression analysis tasks.

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## Core Principles
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