specL
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see specL.
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Bioconductor version: 3.12
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("specL")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("specL")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("specL")| Automatic Workflow | HTML | R Script |
| Introduction to specL | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | MassSpectrometry, Proteomics, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.6), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.5), RSQLite (>= 1.1), seqinr (>= 3.3) |
| Imports | |
| System Requirements | |
| URL | http://bioconductor.org/packages/specL/ |
| Bug Reports | https://github.com/fgcz/specL/issues |
See More
| Suggests | BiocGenerics, BiocStyle(>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | msqc1, NestLink |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | specL_1.24.0.tar.gz |
| Windows Binary | specL_1.24.0.zip |
| macOS 10.13 (High Sierra) | specL_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/specL |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/specL |
| Bioc Package Browser | https://code.bioconductor.org/browse/specL/ |
| Package Short Url | https://bioconductor.org/packages/specL/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |