FragPipe-Analyst

FragPipe-Analyst performs differential expression analysis and visualizes quantitative proteomics data generated by the FragPipe computational platform.

Key Features:

• Quantification workflow support: FragPipe-Analyst supports label-free quantification, tandem mass tags, and data-independent acquisition workflows.
• Missing value imputation: FragPipe-Analyst offers various missing value imputation options for handling incomplete proteomics data.
• Data quality control: FragPipe-Analyst provides data quality control functionalities for assessing quantitative proteomics data.
• Unsupervised clustering: FragPipe-Analyst performs unsupervised clustering analysis of proteomics data.
• Differential expression analysis: FragPipe-Analyst conducts differential expression analysis using Limma.
• Pathway enrichment analysis: FragPipe-Analyst performs gene ontology and pathway enrichment analysis using Enrichr.
• Extended R package functionality: FragPipeAnalystR extends all FragPipe-Analyst functionalities to support site-specific analysis of post-translational modifications.

Scientific Applications:

• Quantitative proteomics downstream analysis: FragPipe-Analyst enables statistical analysis and visualization of quantitative proteomics data from FragPipe output tables.
• Post-translational modification site-specific analysis: FragPipeAnalystR supports site-specific analysis of post-translational modifications for advanced proteomics studies.

Methodology:

FragPipe-Analyst implements differential expression analysis using Limma and performs gene ontology and pathway enrichment analysis using Enrichr.