pepXMLTab

DOI: 10.18129/B9.bioc.pepXMLTab    

Parsing pepXML files and filter based on peptide FDR.

Bioconductor version: Release (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>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("pepXMLTab", version = "3.8")

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 MassSpectrometry, Proteomics, Software
Version 1.16.0
In Bioconductor since BioC 3.0 (R-3.1) (4 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_1.16.0.tar.gz
Windows Binary pepXMLTab_1.16.0.zip
Mac OS X 10.11 (El Capitan) pepXMLTab_1.16.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: