To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PGA")

In most cases, you don't need to download the package archive at all.

PGA

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see PGA.

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

Bioconductor version: 3.2

This package provides functions for construction of customized protein databases based on RNA-Seq data, 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

Maintainer: Bo Wen <wenbo at genomics.cn>, Shaohang Xu <xsh.skye at gmail.com>

Citation (from within R, enter citation("PGA")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PGA")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("PGA")
PDF PGA tutorial
PDF Reference Manual
Text NEWS

Details

biocViews MassSpectrometry, Proteomics, RNASeq, ReportWriting, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.2 (R-3.2) (0.5 years)
License GPL-2
Depends R (>= 3.0.1), IRanges, GenomicRanges, Biostrings(>= 2.26.3), data.table, rTANDEM
Imports Rsamtools(>= 1.10.2), GenomicFeatures(>= 1.19.8), biomaRt(>= 2.17.1), stringr, RCurl, Nozzle.R1, VariantAnnotation(>= 1.7.28), rtracklayer, RSQLite, ggplot2, AnnotationDbi, customProDB(>= 1.7.0), pheatmap
LinkingTo
Suggests BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics, BiocStyle, knitr, R.utils
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source PGA_1.0.0.tar.gz
Windows Binary PGA_1.0.0.zip
Mac OS X 10.6 (Snow Leopard) PGA_1.0.0.tgz
Mac OS X 10.9 (Mavericks) PGA_1.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/PGA/tree/release-3.2
Package Short Url http://bioconductor.org/packages/PGA/
Package Downloads Report Download Stats

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