specL

DOI: 10.18129/B9.bioc.specL    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see specL.

specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Bioconductor version: 3.8

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] (0000-0003-1975-3064), Jonas Grossmann [aut] (0000-0002-6899-9020), Witold E. Wolski [ctb]

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

Installation

To install this package, start R (version "3.5") and enter:

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

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("specL")

 

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

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, Software
Version	1.16.1
In Bioconductor since	BioC 3.0 (R-3.1) (4.5 years)
License	GPL-3
Depends	R (>= 3.3.2), DBI (>= 0.5.1), methods (>= 3.3.2), protViz (>= 0.2.45), RSQLite (>= 1.1.2), seqinr (>= 3.3.3)
Imports
LinkingTo
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
Enhances
URL	https://github.com/fgcz/specL
BugReports	https://github.com/fgcz/specL/issues
Depends On Me
Imports Me
Suggests Me	msqc1
Links To Me
Build Report

Package Archives

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

Source Package	specL_1.16.1.tar.gz
Windows Binary	specL_1.16.1.zip
Mac OS X 10.11 (El Capitan)	specL_1.16.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/specL
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/specL
Package Short Url	http://bioconductor.org/packages/specL/
Package Downloads Report	Download Stats