proteomics-de - LFQ Proteomics Differential Expression Analysis
Analyzes LFQ proteomics data with preprocessing, imputation, and statistical testing for MaxQuant and DIA-NN outputs
Tags
Updated: 2026-03-23proteomicsquantitative proteomicsdifferential expressionstatistical testingdata analysisvisualization
Capabilities
What this skill does
- filter MaxQuant protein groups
- extract DIA-NN protein identifiers
- transform LFQ intensities
- impute missing values
- perform t-test
- calculate FDR correction
- generate PCA plot
- generate volcano plot
- create markdown report
Inputs
- MaxQuant protein groups file
- DIA-NN output file
- sample metadata CSV
- analysis parameters
Outputs
- differential expression results table
- imputed protein groups table
- PCA plot
- volcano plot
- imputation distribution plot
- markdown report
Requirements
- Python3
- pandas
- numpy
- matplotlib
- scikit-learn
- scipy
- seaborn