Automate differential gene expression analysis of bulk RNA-seq data with PyDESeq2.
npx skills add https://github.com/tassiovale/claude-code-kit --skill pydeseq2-tassiovale
Please help me install this Agent Skill. Skill: pydeseq2 Source: https://github.com/tassiovale/claude-code-kit/tree/main/skills/pydeseq2 Command: npx skills add https://github.com/tassiovale/claude-code-kit --skill pydeseq2-tassiovale
This Skill simplifies and automates the differential gene expression analysis using PyDESeq2, offering a streamlined process for RNA-seq data analysis and interpretation.
Run the following command to initiate a DESeq2 analysis: python run_deseq2_analysis.py --counts counts.csv --metadata metadata.csv --design "~condition" --contrast condition treated control --output results/
High-intent search queries and answers about installing and using this skill.
Differential gene expression analysis for bulk RNA-seq data is automated using PyDESeq2, handling normalization, statistical testing, and visualization to compare gene expression between experimental conditions.
Automating RNA-seq data preparation involves filtering low-count genes and removing samples with missing metadata, which this workflow handles natively before running the DESeq2 statistical testing pipeline.
Volcano and MA plots for interpreting RNA-seq differential expression results are generated automatically as part of the visualization workflow after the statistical testing completes.
Yes, PyDESeq2 requires pandas, numpy, scipy, scikit-learn, annData, and formulaic dependencies to perform normalization, statistical testing, and model fitting on bulk RNA-seq count data.
The DESeq2 design formula, such as "~condition", specifies the experimental variable, while the contrast parameter defines the specific groups like treated versus control for differential expression testing.
Victory-HugoPerform differential expression analysis on bulk RNA-seq data with PyDESeq2.
MDheweiIdentify differentially expressed genes between two sample groups from count matrices.
robotlearning123Perform DESeq2 differential expression analysis on bulk RNA-seq count data.
jaechang-hitsPerform differential gene expression analysis on bulk RNA-seq count data with DESeq2.
