specL

DOI: 10.18129/B9.bioc.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 (3.11)

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. 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 "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews MassSpectrometry, Proteomics, Software
Version 1.21.1
In Bioconductor since BioC 3.0 (R-3.1) (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_1.21.1.tar.gz
Windows Binary specL_1.21.1.zip
Mac OS X 10.11 (El Capitan) specL_1.21.1.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 https://bioconductor.org/packages/specL/
Package Downloads Report Download Stats

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