pepXMLTab

DOI: 10.18129/B9.bioc.pepXMLTab    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see pepXMLTab.

Parsing pepXML files and filter based on peptide FDR.

Bioconductor version: 3.8

Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.

Author: Xiaojing Wang

Maintainer: Xiaojing Wang <xiaojing.wang at vanderbilt.edu>

Installation

To install this package, start R (version "3.5") and enter:

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

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("pepXMLTab")

 

PDF	R Script	Introduction to pepXMLTab
PDF		Reference Manual
Text		NEWS

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, Software
Version	1.16.1
In Bioconductor since	BioC 3.0 (R-3.1) (4.5 years)
License	Artistic-2.0
Depends	R (>= 3.0.1)
Imports	XML (>= 3.98-1.1)
LinkingTo
Suggests	RUnit, BiocGenerics
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	pepXMLTab_1.16.1.tar.gz
Windows Binary	pepXMLTab_1.16.1.zip
Mac OS X 10.11 (El Capitan)	pepXMLTab_1.16.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pepXMLTab
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pepXMLTab
Package Short Url	http://bioconductor.org/packages/pepXMLTab/
Package Downloads Report	Download Stats