specL
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Bioconductor version: 3.24 · Package version: 1.47.0
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 <https://fgcz.ch>.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("specL")Details
| Maintainer | Christian Panse <cp@fgcz.ethz.ch> |
| Author | Christian Panse [aut, cre] (ORCID: <https://orcid.org/0000-0003-1975-3064>), Jonas Grossmann [aut] (ORCID: <https://orcid.org/0000-0002-6899-9020>), Christian Trachsel [aut], Witold E. Wolski [ctb] |
| License | GPL-3 |
| URL | http://bioconductor.org/packages/specL/ |
| Bug Reports | https://github.com/fgcz/specL/issues |
| Downloads rank | 544 |
| Source branch | devel |
| biocViews | MassSpectrometry, Proteomics, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | specL_1.47.0.tar.gz |
| Windows binary (x86_64) | specL_1.47.0.zip |
| macOS binary (arm64) | specL_1.47.0.tgz |
| macOS binary (x86_64) | specL_1.47.0.tgz |
Dependencies
Depends: R (>= 4.1), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.7), RSQLite (>= 1.1), seqinr (>= 3.3)
Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4)