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>

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


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


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)
Suggests BiocGenerics, BiocStyle(>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4)
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
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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/
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