specL
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see specL.
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Bioconductor version: 3.9
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("specL")):
Installation
To install this package, start R (version "3.6") 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 | 1.18.1 |
| 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 (>= 0.4), 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_1.18.1.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 |
| 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 3.9 | Source Archive |