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

DOI: 10.18129/B9.bioc.specL    

specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Bioconductor version: Release (3.6)

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 [aut], Christian Panse [aut, cre], Jonas Grossmann [aut], Witold E. Wolski [ctb]

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 Automatic Workflow
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 1.12.0
In Bioconductor since BioC 3.0 (R-3.1) (3 years)
License GPL-3
Depends R (>= 3.3.2), DBI (>= 0.5.1), methods (>= 3.3.2), protViz (>= 0.2.31), RSQLite (>= 1.1.2), seqinr (>= 3.3.3)
Imports
LinkingTo Rcpp (>= 0.12.4)
Suggests BiocGenerics, BiocStyle(>= 2.2.1), knitr (>= 1.15.1), msqc1(>= 1.0.0), plotrix (>= 3.6.4), prozor (>= 0.2.2), RUnit (>= 0.4.31)
SystemRequirements C++11
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.

Source Package specL_1.12.0.tar.gz
Windows Binary specL_1.12.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) specL_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/specL
Package Short Url http://bioconductor.org/packages/specL/
Package Downloads Report Download Stats

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