PGA

DOI: 10.18129/B9.bioc.PGA    

This package is for version 3.10 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: 3.10

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>

Installation

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

if (!requireNamespace("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")

 

PDF	R Script	PGA tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, RNASeq, ReportWriting, Sequencing, Software
Version	1.16.0
In Bioconductor since	BioC 3.2 (R-3.2) (4.5 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, dplyr, processx, readr, seqinr
LinkingTo
Suggests	RMariaDB, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics, BiocStyle, knitr, R.utils
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	PGA_1.16.0.tar.gz
Windows Binary	PGA_1.16.0.zip
Mac OS X 10.11 (El Capitan)	PGA_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PGA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PGA
Package Short Url	https://bioconductor.org/packages/PGA/
Package Downloads Report	Download Stats