PGA: An package for identification of novel peptides by customized database derived from RNA-Seq
Version 1.6.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorShaohang Xu, Bo Wen
Bioconductor views MassSpectrometry Proteomics RNASeq ReportWriting Sequencing Software
Date of publicationNone
MaintainerBo Wen <wenbo@genomics.cn>, Shaohang Xu <xsh.skye@gmail.com>
LicenseGPL-2
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PGA")

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

Functions

OutputNovelJun2 Source code
OutputVarproseq2 Source code
Outputaberrant2 Source code
PrepareAnnotationEnsembl2 Man page Source code
PrepareAnnotationRefseq2 Man page Source code
Sys.which2 Source code
addGeneName4Ensembl Man page Source code
base_transfer Source code
check_parser Source code
createProDB4DenovoRNASeq Man page Source code
dbCreator Man page Source code
dbcat Source code
easyRun Man page Source code
gen_splicmatrix Source code
getNovelTx Source code
get_30aa_splited_seq Source code
highlightjuc Source code
highlightsite Source code
java.executable Source code
juc_type Source code
mut_count_pro Source code
mut_freq_heatmap Source code
mybarplot Source code
parserGear Man page Source code
peptide_number_of_ntx Source code
precursor_error_hist Source code
reportGear Man page Source code
reportIDL Source code
reportJUC Source code
reportNTX Source code
reportSNV Source code
runTandem Man page Source code
spplot Source code
wm_charge_bar Source code
wm_evalue_hist Source code
wm_mass_hist Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/dbCreator.R
R/dbsearch.R
R/dbtool.R
R/easyRun.R
R/report.R
R/reportplot.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/PGA.R
inst/doc/PGA.Rnw
inst/doc/PGA.pdf
inst/extdata
inst/extdata/annotation
inst/extdata/annotation/exon_anno.RData
inst/extdata/annotation/ids.RData
inst/extdata/annotation/procodingseq.RData
inst/extdata/annotation/proseq.RData
inst/extdata/annotation/splicemax.RData
inst/extdata/annotation/txdb.sqlite
inst/extdata/input
inst/extdata/input/PGA.vcf
inst/extdata/input/Trinity.fasta
inst/extdata/input/junctions.bed
inst/extdata/input/mascot.dat
inst/extdata/input/msgfplus.mzid
inst/extdata/input/pga.mgf
inst/extdata/input/transcripts.gtf
inst/parser4PGA.jar
inst/unitTests
inst/unitTests/test_check_parser.R
man
man/PrepareAnnotationEnsembl2.Rd
man/PrepareAnnotationRefseq2.Rd
man/addGeneName4Ensembl.Rd
man/createProDB4DenovoRNASeq.Rd
man/dbCreator.Rd
man/easyRun.Rd
man/parserGear.Rd
man/reportGear.Rd
man/runTandem.Rd
tests
tests/runTests.R
vignettes
vignettes/PGA.Rnw
vignettes/PGA.bib
PGA documentation built on May 20, 2017, 9:24 p.m.