This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see specL.
Bioconductor version: 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] , 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")
):
To install this package, start R (version "3.6") 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 |
R Script | Introduction to specL | |
Reference Manual | ||
Text | NEWS |
biocViews | MassSpectrometry, Proteomics, Software |
Version | 1.18.1 |
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 (>= 0.4), 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 |
Follow Installation instructions to use this package in your R session.
Source Package | specL_1.18.1.tar.gz |
Windows Binary | specL_1.18.1.zip |
Mac OS X 10.11 (El Capitan) | specL_1.18.1.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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