To install this package, start R and enter:

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

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

specL

   

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see specL.

specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Bioconductor version: 3.4

specL provides a function for generating spectra libraries which can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software.

Author: Christian Trachsel <christian.trachsel at fgcz.uzh.ch>, Christian Panse <cp at fgcz.ethz.ch>, Jonas Grossmann <jg at fgcz.ethz.ch>, Witold E. Wolski <wewolski at gmail.com>

Maintainer: Christian Panse <cp at fgcz.ethz.ch>, Witold E. Wolski <wewolski at gmail.com>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("specL")

 

PDF R Script Introduction to specL
HTML R Script Computing Dynamic SWATH Windows
HTML R Script Retention Time Prediction using the ssrc Method
PDF   Reference Manual
Text   NEWS

Details

biocViews MassSpectrometry, Proteomics, Software
Version 1.8.0
In Bioconductor since BioC 3.0 (R-3.1) (2.5 years)
License GPL-3
Depends R (>= 3.3), methods, DBI, RSQLite, seqinr, protViz (>= 0.2.15)
Imports
LinkingTo Rcpp (>= 0.12.4)
Suggests RUnit, BiocGenerics, BiocStyle, plotrix, knitr, msqc1(>= 1.0.0)
SystemRequirements
Enhances
URL https://github.com/fgcz/specL
BugReports https://github.com/fgcz/specL/issues
Depends On Me
Imports Me
Suggests Me msqc1
Build Report  

Package Archives

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

Package Source specL_1.8.0.tar.gz
Windows Binary specL_1.8.0.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) specL_1.8.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/specL/tree/release-3.4
Package Short Url http://bioconductor.org/packages/specL/
Package Downloads Report Download Stats

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