MSGFplus

DOI: 10.18129/B9.bioc.MSGFplus    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.14 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see MSGFplus.

An interface between R and MS-GF+

Bioconductor version: 3.14

This package contains function to perform peptide identification using the MS-GF+ algorithm. The package contains functionality for building up a parameter set both in code and through a simple GUI, as well as running the algorithm in batches, potentially asynchronously.

Author: Thomas Lin Pedersen

Maintainer: Thomas Lin Pedersen <thomasp85 at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MSGFplus")

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("MSGFplus")

 

HTML	R Script	Using MSGFgui
PDF		Reference Manual
Text		NEWS

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, Software
Version	1.28.0
In Bioconductor since	BioC 3.0 (R-3.1) (7.5 years)
License	GPL (>= 2)
Depends	methods
Imports	mzID, ProtGenerics
LinkingTo
Suggests	knitr, testthat
SystemRequirements	Java (>= 1.7)
Enhances
URL
Depends On Me
Imports Me	MSGFgui
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MSGFplus_1.28.0.tar.gz
Windows Binary	MSGFplus_1.28.0.zip
macOS 10.13 (High Sierra)	MSGFplus_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MSGFplus
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MSGFplus
Package Short Url	https://bioconductor.org/packages/MSGFplus/
Package Downloads Report	Download Stats