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specL

This is the development version of specL; for the stable release version, see specL.

specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Automatic specL Workflow HTML R Script
Introduction to specL HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews MassSpectrometry, Proteomics, Software
Version 1.37.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL-3
Depends R (>= 4.1), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.7), RSQLite (>= 1.1), seqinr (>= 3.3)
Imports
System Requirements
URL http://bioconductor.org/packages/specL/
Bug Reports https://github.com/fgcz/specL/issues
See More
Suggests BiocGenerics, BiocStyle(>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me msqc1, NestLink
Links To Me
Build Report Build Report

Package Archives

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

Source Package specL_1.37.0.tar.gz
Windows Binary specL_1.37.0.zip
macOS Binary (x86_64) specL_1.37.0.tgz
macOS Binary (arm64) specL_1.37.0.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