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pepXMLTab

Parsing pepXML files and filter based on peptide FDR.


Bioconductor version: Release (3.18)

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 (version "4.3") and enter:


if (!require("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")
Introduction to pepXMLTab PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ImmunoOncology, MassSpectrometry, Proteomics, Software
Version 1.36.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License Artistic-2.0
Depends R (>= 3.0.1)
Imports XML (>= 3.98-1.1)
System Requirements
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Suggests RUnit, BiocGenerics
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Package Archives

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

Source Package pepXMLTab_1.36.0.tar.gz
Windows Binary pepXMLTab_1.36.0.zip
macOS Binary (x86_64) pepXMLTab_1.36.0.tgz
macOS Binary (arm64) pepXMLTab_1.36.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pepXMLTab
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pepXMLTab
Bioc Package Browser https://code.bioconductor.org/browse/pepXMLTab/
Package Short Url https://bioconductor.org/packages/pepXMLTab/
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