This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see specL.
Bioconductor version: 3.8
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 Trachsel [aut], Christian Panse [aut, cre] (0000-0003-1975-3064), Jonas Grossmann [aut] (0000-0002-6899-9020), Witold E. Wolski [ctb]
Maintainer: Christian Panse <cp at fgcz.ethz.ch>, Witold E. Wolski <wewolski at gmail.com>
Citation (from within R,
enter citation("specL")
):
To install this package, start R (version "3.5") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("specL")
For older versions of R, please refer to the appropriate Bioconductor release.
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 |
R Script | Introduction to specL | |
HTML | R Script | Retention Time Prediction using the ssrc Method |
Reference Manual | ||
Text | NEWS |
biocViews | ImmunoOncology, MassSpectrometry, Proteomics, Software |
Version | 1.16.1 |
In Bioconductor since | BioC 3.0 (R-3.1) (4.5 years) |
License | GPL-3 |
Depends | R (>= 3.3.2), DBI (>= 0.5.1), methods (>= 3.3.2), protViz (>= 0.2.45), RSQLite (>= 1.1.2), seqinr (>= 3.3.3) |
Imports | |
LinkingTo | |
Suggests | BiocGenerics, BiocStyle(>= 2.2.1), knitr (>= 1.15.1), msqc1(>= 1.0.0), plotrix (>= 3.6.4), prozor (>= 0.2.2), 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 |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | specL_1.16.1.tar.gz |
Windows Binary | specL_1.16.1.zip |
Mac OS X 10.11 (El Capitan) | specL_1.16.1.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 | http://bioconductor.org/packages/specL/ |
Package Downloads Report | Download Stats |
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