MSGFplus

This package is for version 3.9 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: 3.9

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>

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

Installation

To install this package, start R (version "3.6") 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")
Using MSGFgui HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ImmunoOncology, MassSpectrometry, Proteomics, Software
Version 1.18.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL (>= 2)
Depends methods
Imports mzID, ProtGenerics
System Requirements Java (>= 1.7)
URL
See More
Suggests gWidgets, knitr, testthat
Linking To
Enhances
Depends On Me proteomics
Imports Me MSGFgui
Suggests Me RforProteomics
Links To Me
Build Report Build Report

Package Archives

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

Source Package MSGFplus_1.18.0.tar.gz
Windows Binary MSGFplus_1.18.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) MSGFplus_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MSGFplus
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MSGFplus
Bioc Package Browser https://code.bioconductor.org/browse/MSGFplus/
Package Short Url https://bioconductor.org/packages/MSGFplus/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive