To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MSnID")

In most cases, you don't need to download the package archive at all.

MSnID

DOI: 10.18129/B9.bioc.MSnID    

Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

Bioconductor version: Release (3.6)

Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.

Author: Vlad Petyuk with contributions from Laurent Gatto

Maintainer: Vlad Petyuk <petyuk at gmail.com>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MSnID")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MSnID")

 

PDF R Script MSnID Package for Handling MS/MS Identifications
PDF   Reference Manual
Text   NEWS

Details

biocViews MassSpectrometry, Proteomics, Software
Version 1.11.0
In Bioconductor since BioC 3.0 (R-3.1) (3 years)
License Artistic-2.0
Depends R (>= 2.10), Rcpp
Imports MSnbase(>= 1.12.1), mzID(>= 1.3.5), R.cache, foreach, doParallel, parallel, methods, iterators, data.table, Biobase, ProtGenerics, reshape2, dplyr, mzR
LinkingTo
Suggests BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me RforProteomics
Build Report  

Package Archives

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

Source Package MSnID_1.11.0.tar.gz
Windows Binary MSnID_1.11.0.zip
Mac OS X 10.11 (El Capitan) MSnID_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MSnID
Package Short Url http://bioconductor.org/packages/MSnID/
Package Downloads Report Download Stats

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