To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("xcms")
In most cases, you don't need to download the package archive at all.
xcms
LC/MS and GC/MS Data Analysis
Bioconductor version: 3.0
Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.
Author: Colin A. Smith <csmith at scripps.edu>, Ralf Tautenhahn <rtautenh at gmail.com>, Steffen Neumann <sneumann at ipb-halle.de>, Paul Benton <hpbenton at scripps.edu>, Christopher Conley <cjconley at ucdavis.edu>
Maintainer: Ralf Tautenhahn <rtautenh at gmail.com>
Citation (from within R,
enter citation("xcms")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("xcms")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("xcms")
| R Script | Grouping FTICR-MS data with xcms | |
| R Script | Installation Instructions for xcms | |
| R Script | LC/MS Preprocessing and Analysis with xcms | |
| R Script | Processing Tandem-MS and MS$^n$ data with xcms | |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | MassSpectrometry, Metabolomics, Software |
| Version | 1.42.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier |
| License | GPL (>= 2) + file LICENSE |
| Depends | R (>= 2.14.0), methods, mzR(>= 1.1.6), BiocGenerics, Biobase |
| Imports | |
| LinkingTo | |
| Suggests | faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet(>= 1.5.2), RANN, RUnit |
| SystemRequirements | |
| Enhances | Rgraphviz, Rmpi, XML |
| URL | http://metlin.scripps.edu/download/ and https://github.com/sneumann/xcms |
| Depends On Me | CAMERA, faahKO, flagme, Metab, metaMS |
| Imports Me | CAMERA, cosmiq, MAIT, Risa |
| Suggests Me | MassSpecWavelet, msdata, RforProteomics, RMassBank |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | xcms_1.42.0.tar.gz |
| Windows Binary | xcms_1.42.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | xcms_1.42.0.tgz |
| Mac OS X 10.9 (Mavericks) | xcms_1.42.0.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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