rnaseq-differential-expression
CommunityDetect differential expression between groups with robust DE methods.
AuthorMDhewei
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Identify genes that are differentially expressed between two biological groups using a gene count or expression matrix, supporting DESeq2-style analysis via pydeseq2 as well as faster non-parametric tests on normalized data, and deliver publication-ready results and visualizations.
Core Features & Use Cases
- DE methods: DESeq2-style via pydeseq2, Welch's t-test, and Mann-Whitney U to accommodate raw counts or normalized data.
- Outputs: full differential expression results, a significant genes list, volcano and MA plots, and a top-genes heatmap; all designed to feed into downstream analyses like go-analysis-for-gene-list and gsea-for-ranked-gene-list.
- Inputs & workflow: requires a gene-by-sample count matrix and a metadata table with sample and group columns; define group-a and group-b to compare, perform low-expression filtering, and generate comprehensive reports and figures.
Quick Start
Provide a counts matrix and metadata, specify group-a and group-b labels, and run the script to generate DE results and visualizations.
Dependency Matrix
Required Modules
pydeseq2pandasnumpyscipymatplotlibseaborn
Components
scripts
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Please help me install this Skill: Name: rnaseq-differential-expression Download link: https://github.com/MDhewei/bioinfor-claw/archive/main.zip#rnaseq-differential-expression Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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