PyDESeq2

When to Use This Skill

This skill should be used when:

• Analyzing bulk RNA-seq count data for differential expression
• Comparing gene expression between experimental conditions (e.g., treated vs control)
• Performing multi-factor designs accounting for batch effects or covariates
• Converting R-based DESeq2 workflows to Python
• Integrating differential expression analysis into Python-based pipelines
• Users mention "DESeq2", "differential expression", "RNA-seq analysis", or "PyDESeq2"

Quick Start Workflow

For users who want to perform a standard differential expression analysis:

import pandas as pd
from pydeseq2.dds import DeseqDataSet
from pydeseq2.ds import DeseqStats

## 2. Filter low-count genes

genes_to_keep = counts_df.columns[counts_df.sum(axis=0) >= 10]
counts_df = counts_df[genes_to_keep]