Proteomics - Label-free quantitative proteomics analysis toolkit
Analyzes label-free quantitative proteomics data using R scripts for normalization, visualization, pathway analysis and protein list cross-referencing
Tags
Updated: 2026-02-11Capabilities
Typical Inputs
Typical Outputs
What this skill does
- normalize protein data
- create volcano plots
- generate heatmaps
- run PCA analysis
- perform pathway enrichment
- query protein lists
- create Excel reports
- analyze matrisome proteins
- identify SASP factors
Inputs
- protein intensity data
- sample metadata
- comparison results
- q-value threshold
- fold-change cutoff
- organism specification
- reference protein lists
- R scripts directory
- project working directory
Outputs
- TIFF plot files
- Excel report tables
- pathway analysis results
- protein list matches
- normalized data files
- sample correlation plots
- volcano plot images
- heatmap visualizations
Requirements
- R environment installed
- specific directory structure
- reference data files available
- project working directory set
- data/ subdirectory with input files
- output/ subdirectory for results
- Proteomics skill directory accessible