specL

DOI: 10.18129/B9.bioc.specL  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see specL.

specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Bioconductor version: 3.16

provides a functions 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. The package is developed, tested and used at the Functional Genomics Center Zurich .

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 "4.2") and enter:

if (!require("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 specL Workflow
HTML	R Script	Introduction to specL
PDF		Reference Manual
Text		NEWS

Details

biocViews	MassSpectrometry, Proteomics, Software
Version	1.32.1
In Bioconductor since	BioC 3.0 (R-3.1) (8.5 years)
License	GPL-3
Depends	R (>= 3.6), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.5), 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_1.32.1.tar.gz
Windows Binary	specL_1.32.1.zip
macOS Binary (x86_64)	specL_1.32.1.tgz
macOS Binary (arm64)	specL_1.32.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/specL
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/specL
Bioc Package Browser	https://code.bioconductor.org/browse/specL/
Package Short Url	https://bioconductor.org/packages/specL/
Package Downloads Report	Download Stats