run_deseq2_analysis

This script performs a complete differential expression analysis using PyDESeq2. It can be used as a template for standard RNA-seq DEA workflows.

Skills
Scientific
1

What it does and how to use it

A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

Install the skill (command above).
In Claude Code, describe what you need - the skill turns on by itself when the context fits.
No commands to memorize: you talk in plain language and the skill does the rest.

Install (Claude Code)

mkdir -p .claude/skills/run-deseq2-analysis && curl -fsSL https://doutorai.pt/data/lib/skills__run-deseq2-analysis.md -o .claude/skills/run-deseq2-analysis/SKILL.md

Paste this command into the terminal, in your project folder, and the component installs automatically.

Content

#!/usr/bin/env python3
"""
PyDESeq2 Analysis Script

This script performs a complete differential expression analysis using PyDESeq2.
It can be used as a template for standard RNA-seq DEA workflows.

Usage:
    python run_deseq2_analysis.py --counts counts.csv --metadata metadata.csv \
           --design "~condition" --contrast condition treated control \
           --output results/

Requirements:
    - pydeseq2
    - pandas
    - matplotlib (optional, for plots)
"""

import argparse
import os
import pickle
import sys
from pathlib import Path

import pandas as pd

try:
    from pydeseq2.dds 

- 🔒 Full content on the Pro plan (€7.99/month) -

Need help with Claude Code?

Ask Dr AI - it explains things simply.

Need a tailor-made solution?

Not sure where to start with AI in your business? Get a free assessment and a tailored plan - no commitment.

Save hours every week with AI, no hassle

Doutor AI gives you 1,859 ready-to-copy AI prompts, by industry and in plain English - plus a complete technical library for those who want to go further.

See plans