To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("specL")
In most cases, you don't need to download the package archive at all.
specL
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Bioconductor version: 3.0
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 <christian.trachsel at fgcz.uzh.ch>, Christian Panse <cp at fgcz.ethz.ch>, Jonas Grossmann <jg at fgcz.ethz.ch>
Maintainer: Christian Panse <cp at fgcz.ethz.ch>
Citation (from within R,
enter citation("specL")):
Installation
To install this package, start R and enter:
source("http://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 | specL | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | MassSpectrometry, Proteomics, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | GPL-3 |
| Depends | R (>= 3.0.2), methods, DBI, RSQLite, seqinr, protViz (>= 0.2.5) |
| Imports | |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics, BiocStyle, BiocParallel |
| SystemRequirements | |
| Enhances | |
| URL | http://www.bioconductor.org/packages/devel/bioc/html/specL.html |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | specL_1.0.0.tar.gz |
| Windows Binary | specL_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | specL_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | specL_1.0.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: support.bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2015, Bioconductor
