To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("mzID")
In most cases, you don't need to download the package archive at all.
mzID
An mzIdentML parser for R
Bioconductor version: 3.0
A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.
Author: Thomas Lin Pedersen, Vladislav A Petyuk with contributions from Laurent Gatto and Sebastian Gibb.
Maintainer: Thomas Lin Pedersen <thomasp85 at gmail.com>
Citation (from within R,
enter citation("mzID")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("mzID")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("mzID")
| R Script | Using mzID | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, MassSpectrometry, Proteomics, Software |
| Version | 1.4.1 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | GPL (>= 2) |
| Depends | methods |
| Imports | XML, plyr, parallel, doParallel, foreach, iterators |
| LinkingTo | |
| Suggests | knitr, testthat |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | MSGFgui, MSGFplus, MSnbase, MSnID, Pbase |
| Suggests Me | mzR, RforProteomics |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | mzID_1.4.1.tar.gz |
| Windows Binary | mzID_1.4.1.zip |
| Mac OS X 10.6 (Snow Leopard) | mzID_1.4.1.tgz |
| Mac OS X 10.9 (Mavericks) | mzID_1.4.1.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
