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

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.

Author
Shaohang Xu, Bo Wen
Date of publication
None
Maintainer
Bo Wen <wenbo@genomics.cn>, Shaohang Xu <xsh.skye@gmail.com>
License
GPL-2
Version
1.4.0

View on Bioconductor

Man pages

addGeneName4Ensembl
Add gene nemes
createProDB4DenovoRNASeq
Create protein database based on the transcripts from de novo...
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

Files in this package

PGA/DESCRIPTION
PGA/NAMESPACE
PGA/NEWS
PGA/R
PGA/R/dbCreator.R
PGA/R/dbsearch.R
PGA/R/dbtool.R
PGA/R/easyRun.R
PGA/R/report.R
PGA/R/reportplot.R
PGA/build
PGA/build/vignette.rds
PGA/inst
PGA/inst/CITATION
PGA/inst/doc
PGA/inst/doc/PGA.R
PGA/inst/doc/PGA.Rnw
PGA/inst/doc/PGA.pdf
PGA/inst/extdata
PGA/inst/extdata/annotation
PGA/inst/extdata/annotation/exon_anno.RData
PGA/inst/extdata/annotation/ids.RData
PGA/inst/extdata/annotation/procodingseq.RData
PGA/inst/extdata/annotation/proseq.RData
PGA/inst/extdata/annotation/splicemax.RData
PGA/inst/extdata/annotation/txdb.sqlite
PGA/inst/extdata/input
PGA/inst/extdata/input/PGA.vcf
PGA/inst/extdata/input/Trinity.fasta
PGA/inst/extdata/input/junctions.bed
PGA/inst/extdata/input/mascot.dat
PGA/inst/extdata/input/msgfplus.mzid
PGA/inst/extdata/input/pga.mgf
PGA/inst/extdata/input/transcripts.gtf
PGA/inst/parser4PGA.jar
PGA/inst/unitTests
PGA/inst/unitTests/test_check_parser.R
PGA/man
PGA/man/PrepareAnnotationEnsembl2.Rd
PGA/man/PrepareAnnotationRefseq2.Rd
PGA/man/addGeneName4Ensembl.Rd
PGA/man/createProDB4DenovoRNASeq.Rd
PGA/man/dbCreator.Rd
PGA/man/easyRun.Rd
PGA/man/parserGear.Rd
PGA/man/reportGear.Rd
PGA/man/runTandem.Rd
PGA/tests
PGA/tests/runTests.R
PGA/vignettes
PGA/vignettes/PGA.Rnw
PGA/vignettes/PGA.bib