specL
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Bioconductor version: 3.23 · Package version: 1.46.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | MassSpectrometry, Proteomics, Software |
| Package Short Url | https://bioconductor.org/packages/specL/ |
Citation
From within R, enter citation("specL"):
Christian Panse, Jonas Grossmann, Christian Trachsel. specL: specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics. doi:10.18129/B9.bioc.specL, R package version 1.46.0, https://bioconductor.org/packages/specL.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | specL_1.46.0.tar.gz |
| Windows binary (x86_64) | specL_1.46.0.zip |
| macOS binary (arm64) | specL_1.46.0.tgz |
| macOS binary (x86_64) | specL_1.46.0.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)