PGA

DOI:10.18129/B9.bioc.PGA

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, seePGA.

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

Bioconductor version: 3.11

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 , Shaohang Xu

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("PGA")

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

Documentation

查看文档的版本包age 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	1.18.1
In Bioconductor since	BioC 3.2 (R-3.2) (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

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	PGA_1.18.1.tar.gz
Windows Binary	PGA_1.18.1.zip
macOS 10.13 (High Sierra)	PGA_1.18.1.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	//www.andersvercelli.com/packages/PGA/
Package Downloads Report	Download Stats