This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see specL.
Bioconductor version: 3.11
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")
):
To install this package, start R (version "4.0") 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 | 1.22.0 |
In Bioconductor since | BioC 3.0 (R-3.1) (6 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 |
Follow Installation instructions to use this package in your R session.
Source Package | specL_1.22.0.tar.gz |
Windows Binary | specL_1.22.0.zip |
macOS 10.13 (High Sierra) | specL_1.22.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/specL |
Source Repository (Developer Access) | git clone [email protected]:packages/specL |
Package Short Url | https://bioconductor.org/packages/specL/ |
Package Downloads Report | Download Stats |
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