MSGFplus

DOI: 10.18129/B9.bioc.MSGFplus    

This is the development version of MSGFplus; to use it, please install the devel version of Bioconductor.

An interface between R and MS-GF+

Bioconductor version: Development (3.10)

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.19.0
In Bioconductor since BioC 3.0 (R-3.1) (5 years)
License GPL (>= 2)
Depends methods
Imports mzID, ProtGenerics
LinkingTo
Suggests gWidgets, knitr, testthat
SystemRequirements Java (>= 1.7)
Enhances
URL
Depends On Me proteomics
Imports Me MSGFgui
Suggests Me RforProteomics
Links To Me
Build Report  

Package Archives

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

Source Package MSGFplus_1.19.0.tar.gz
Windows Binary MSGFplus_1.19.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) MSGFplus_1.19.0.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

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