specL

DOI: 10.18129/B9.bioc.specL    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see specL.

specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Bioconductor version: 3.10

provides a function for generating spectra libraries that 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 Panse [aut, cre] , Jonas Grossmann [aut] , Christian Trachsel [aut], Witold E. Wolski [ctb]

Maintainer: Christian Panse <cp at fgcz.ethz.ch>

Installation

To install this package, start R (version "3.6") 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
PDF	R Script	Introduction to specL
PDF		Reference Manual
Text		NEWS

Details

biocViews	MassSpectrometry, Proteomics, Software
Version	1.20.0
In Bioconductor since	BioC 3.0 (R-3.1) (5.5 years)
License	GPL-3
Depends	R (>= 3.6), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.4), RSQLite (>= 1.1), seqinr (>= 3.3)
Imports
LinkingTo
Suggests	BiocGenerics, BiocStyle(>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4)
SystemRequirements
Enhances
URL	http://bioconductor.org/packages/specL/
BugReports	https://github.com/fgcz/specL/issues
Depends On Me
Imports Me
Suggests Me	msqc1, NestLink
Links To Me
Build Report

Package Archives

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

Source Package	specL_1.20.0.tar.gz
Windows Binary	specL_1.20.0.zip
Mac OS X 10.11 (El Capitan)	specL_1.20.0.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	https://bioconductor.org/packages/specL/
Package Downloads Report	Download Stats