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 (3.9)

provides a function for generating spectra libraries which 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] (<https://orcid.org/0000-0003-1975-3064>), Jonas Grossmann [aut] (<https://orcid.org/0000-0002-6899-9020>), 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 "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("specL", version = "3.9")

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
HTML R Script Computing Dynamic SWATH Windows
PDF R Script Introduction to specL
HTML R Script Retention Time Prediction using the ssrc Method
PDF   Reference Manual
Text   NEWS

Details

biocViews MassSpectrometry, Proteomics, Software
Version 1.17.3
In Bioconductor since BioC 3.0 (R-3.1) (4.5 years)
License GPL-3
Depends R (>= 3.6), DBI (>= 0.5.1), methods (>= 3.3.2), protViz (>= 0.4.0), RSQLite (>= 1.1.2), seqinr (>= 3.3.3)
Imports
LinkingTo
Suggests BiocGenerics, BiocStyle(>= 2.2.1), knitr (>= 1.15.1), msqc1(>= 1.0.0), rmarkdown, RUnit (>= 0.4.31)
SystemRequirements
Enhances
URL https://github.com/fgcz/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_1.17.3.tar.gz
Windows Binary specL_1.17.1.zip
Mac OS X 10.11 (El Capitan) specL_1.17.3.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 http://bioconductor.org/packages/specL/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: