xcms
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see xcms.
LC-MS and GC-MS Data Analysis
Bioconductor version: 3.11
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>, Johannes Rainer <Johannes.Rainer at eurac.edu>, Michael Witting <michael.witting at helmholtz-muenchen.de>
Maintainer: Steffen Neumann <sneumann at ipb-halle.de>
citation("xcms")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("xcms")
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("xcms")| Grouping FTICR-MS data with xcms | HTML | R Script |
| LC-MS/MS data analysis with xcms | HTML | R Script |
| LCMS data preprocessing and analysis with xcms | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Metabolomics, Software |
| Version | 3.10.2 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 19 years) |
| License | GPL (>= 2) + file LICENSE |
| Depends | R (>= 2.14.0), methods, Biobase, BiocParallel(>= 1.8.0), MSnbase(>= 2.9.3), MSnbase(<= 2.15.0) |
| Imports | mzR(>= 2.19.5), BiocGenerics, ProtGenerics(>= 1.17.2), lattice, RColorBrewer, plyr, RANN, MassSpecWavelet(>= 1.5.2), S4Vectors, robustbase, IRanges, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/sneumann/xcms |
| Bug Reports | https://github.com/sneumann/xcms/issues/new |
See More
| Suggests | BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata(>= 0.25.1), ncdf4, rgl, microbenchmark, testthat, pander, magrittr, multtest, MALDIquant, pheatmap |
| Linking To | |
| Enhances | Rgraphviz, Rmpi, XML |
| Depends On Me | CAMERA, faahKO, flagme, IPO, LOBSTAHS, Metab, metaMS, ncGTW, proFIA, PtH2O2lipids |
| Imports Me | CAMERA, cliqueMS, cosmiq, MAIT, Risa |
| Suggests Me | CluMSID, MassSpecWavelet, msdata, msPurity, mtbls2, RforProteomics, RMassBank |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | xcms_3.10.2.tar.gz |
| Windows Binary | xcms_3.10.2.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | |
| Source Repository | git clone https://git.bioconductor.org/packages/xcms |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/xcms |
| Bioc Package Browser | https://code.bioconductor.org/browse/xcms/ |
| Package Short Url | https://bioconductor.org/packages/xcms/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |