To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("specL")
In most cases, you don't need to download the package archive at all.
specL
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specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Bioconductor version: Release (3.5)
specL 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], Jonas Grossmann [aut], Witold E. Wolski [ctb]
Maintainer: Christian Panse <cp at fgcz.ethz.ch>, Witold E. Wolski <wewolski at gmail.com>
Citation (from within R,
enter citation("specL")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("specL")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("specL")
| R Script | Introduction to specL | |
| HTML | R Script | Automatic Workflow |
| HTML | R Script | Computing Dynamic SWATH Windows |
| HTML | R Script | Retention Time Prediction using the ssrc Method |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | MassSpectrometry, Proteomics, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (3 years) |
| License | GPL-3 |
| Depends | R (>= 3.3.2), DBI (>= 0.5.1), methods (>= 3.3.2), protViz (>= 0.2.28), RSQLite (>= 1.1.2), seqinr (>= 3.3.3) |
| Imports | |
| LinkingTo | Rcpp (>= 0.12.4) |
| 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) |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/fgcz/specL |
| BugReports | https://github.com/fgcz/specL/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | msqc1 |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | specL_1.10.0.tar.gz |
| Windows Binary | specL_1.10.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | specL_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/specL |
| Package Short Url | http://bioconductor.org/packages/specL/ |
| Package Downloads Report | Download Stats |
Documentation »
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