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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("iontree")
In most cases, you don't need to download the package archive at all.
iontree
Data management and analysis of ion trees from ion-trap mass spectrometry
Bioconductor version: 3.0
Ion fragmentation provides structural information for metabolite identification. This package provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.
Author: Mingshu Cao
Maintainer: Mingshu Cao <mingshu.cao at agresearch.co.nz>
Citation (from within R,
enter citation("iontree")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("iontree")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("iontree")
| R Script | MSn | |
| Reference Manual | ||
| Text | LICENSE |
Details
| biocViews | MassSpectrometry, Metabolomics, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | GPL-2 |
| Depends | methods, rJava, RSQLite, XML |
| Imports | |
| LinkingTo | |
| Suggests | iontreeData |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | iontree_1.12.0.tar.gz |
| Windows Binary | iontree_1.12.0.zip |
| Mac OS X 10.6 (Snow Leopard) | iontree_1.12.0.tgz |
| Mac OS X 10.9 (Mavericks) | iontree_1.12.0.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
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