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PGA (version 1.2.2)

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

Description

This package provides functions for construction of customized protein databases based on RNA-Seq data with/without genome guided, database searching, post-processing and report generation. This kind of customized protein database includes both the reference database (such as Refseq or ENSEMBL) and the novel peptide sequences form RNA-Seq data.

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Version

Version

1.2.2

License

GPL-2

Maintainer

Bo Wen

Last Published

February 15th, 2017

Functions in PGA (1.2.2)

addGeneName4Ensembl

Add gene nemes
reportGear

The main function for report generation
PrepareAnnotationEnsembl2

Prepare annotation from ENSEMBL
runTandem

run X!Tandem
PrepareAnnotationRefseq2

Prepare annotation from Refseq
easyRun

easyRun
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
parserGear

Post-processing for the identification result