# Post-Translational Modification Enrichment, Integration, and Matching Analysis

## Documentation for package ‘PEIMAN2’ version 1.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

exmplData1 | Example dataset1
exmplData2 | Example dataset 2
getTaxonomyName | Return the exact taxonomy name for list of protein
mod_ont | Database of protein modifications
plotEnrichment | Plot and match singular enrichment results
plotPSEA | Plot the results of protein set enrichment analysis (PSEA)
plotRunningScore | Plot running score plot for the results of psea
psea2mass | Translate PSEA results for Mass Spectrometry searching tools
ptmlist | Controlled vocabulary for post-translational modifications (PTM) terms
runEnrichment | Run singular enrichment analysis (SEA) for a given list of protein
runPSEA | Run Protein Set Enrichment Analysis (PSEA)
sea2mass | Translate SEA results for Mass Spectrometry searching tools
update_peiman_database | Download and cache PEIMAN2 external data files