specL
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see specL.
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Bioconductor version: 3.7
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 Trachsel [aut], Christian Panse [aut, cre] (0000-0003-1975-3064), Jonas Grossmann [aut] (0000-0002-6899-9020), Witold E. Wolski [ctb]
Maintainer: Christian Panse <cp at fgcz.ethz.ch>, Witold E. Wolski <wewolski at gmail.com>
citation("specL")):
Installation
To install this package, start R (version "3.5") 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 |
| Computing Dynamic SWATH Windows | HTML | R Script |
| Introduction to specL | R Script | |
| Retention Time Prediction using the ssrc Method | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | MassSpectrometry, Proteomics, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.3.2), DBI (>= 0.5.1), methods (>= 3.3.2), protViz (>= 0.2.45), RSQLite (>= 1.1.2), seqinr (>= 3.3.3) |
| Imports | |
| System Requirements | |
| URL | https://github.com/fgcz/specL |
| Bug Reports | https://github.com/fgcz/specL/issues |
See More
| Suggests | BiocGenerics, BiocStyle(>= 2.2.1), knitr (>= 1.15.1), msqc1(>= 1.0.0), plotrix (>= 3.6.4), prozor (>= 0.2.2), RUnit (>= 0.4.31) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | msqc1 |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | specL_1.14.0.tar.gz |
| Windows Binary | specL_1.14.0.zip |
| Mac OS X 10.11 (El Capitan) | specL_1.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/specL |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/specL |
| Package Short Url | https://bioconductor.org/packages/specL/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.7 | Source Archive |