PGA

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see PGA.

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


Bioconductor version: 3.9

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

Maintainer: Bo Wen <wenbostar at gmail.com>, Shaohang Xu <xsh.skye at gmail.com>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PGA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

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

Details

biocViews ImmunoOncology, MassSpectrometry, Proteomics, RNASeq, ReportWriting, Sequencing, Software
Version 1.14.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL-2
Depends R (>= 3.5.0), IRanges, GenomicRanges, Biostrings(>= 2.26.3), data.table, rTANDEM
Imports S4Vectors(>= 0.9.25), 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(>= 1.21.5), pheatmap
System Requirements
URL
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Suggests RMariaDB, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics, BiocStyle, knitr, R.utils
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Depends On Me
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Build Report Build Report

Package Archives

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

Source Package PGA_1.14.0.tar.gz
Windows Binary PGA_1.14.0.zip
Mac OS X 10.11 (El Capitan) PGA_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PGA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PGA
Bioc Package Browser https://code.bioconductor.org/browse/PGA/
Package Short Url https://bioconductor.org/packages/PGA/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive