# An package for identification of novel peptides by customized database derived from RNA-Seq

## Documentation for package ‘PGA’ version 1.20.0

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

## Help Pages

addGeneName4Ensembl | Add gene nemes
buildFusionProteinDB | Create customized protein database from fusion events
createProDB4DenovoRNASeq | Create protein database based on the transcripts from de novo reconstruction of transcriptome from RNA-seq data
dbCreator | Create customized protein database from RNA-Seq data
easyRun | easyRun
parserGear | Post-processing for the identification result
PrepareAnnotationEnsembl2 | Prepare annotation from ENSEMBL
PrepareAnnotationRefseq2 | Prepare annotation from Refseq
reportGear | The main function for report generation
runTandem | run X!Tandem