specL

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see specL.

specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Bioconductor version: 3.6

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 (version "3.4") 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")

Introduction to specL PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews MassSpectrometry, Proteomics, Software

Version 1.12.0

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 (>= 0.2.31), RSQLite (>= 1.1.2), seqinr (>= 3.3.3)

Imports

System Requirements C++11

URL https://github.com/fgcz/specL

Bug Reports https://github.com/fgcz/specL/issues

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 Rcpp (>= 0.12.4)

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_1.12.0.tar.gz

Windows Binary specL_1.12.0.zip (32- & 64-bit)

Mac OS X 10.11 (El Capitan) specL_1.12.0.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 3.6 Source Archive