proteomics-de - Differential Protein Abundance Testing
Statistical testing for differentially abundant proteins between experimental conditions
Tags
Updated: 2026-03-20Capabilities
Typical Inputs
Typical Outputs
What this skill does
- perform MSstats comparison
- run limma t-tests
- handle missing values
- run scipy t-tests
- generate volcano plots
- create heatmaps
Inputs
- protein matrix CSV file
- comparison matrix
- condition groups
- FDR threshold
- FC threshold
Outputs
- differential results table
- statistics CSV file
- volcano plot image
- analysis report
- result JSON file
Requirements
- Python environment
- R packages (MSstats, limma, proDA)
- numpy
- pandas
- scipy
- statsmodels