RAMClustR specifications

Information


Unique identifier OMICS_14258
Name RAMClustR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format XCMS
Output data similarity matrix, spectra, specData (MS level data after condensing feature intensities into spectral intensities)
Output format MSP
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Broeckling Corey <>

Publication for RAMClustR

RAMClustR in publications

 (7)
PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] from the feeding experiment). msclust [] has the same general features as the others, but it was developed in the c++ language and it is optimized to work with the output files of metalign. ramclustr [] was developed in matlab and implemented in r, accepting directly the output of xcms. the authors suggest the use of a workflow consisting of data acquisition under both low and high […]

PMCID: 5347386
PMID: 28287618
DOI: 10.1038/srep44394

[…] calculated among replicate injections (n = 2). due to normalization of the dataset, the quantitation of each molecular feature is described using relative abundance (ra). features were grouped using ramclustr, which groups features into spectra based coelution and covariance across the full dataset, whereby spectra are used to determine the identity of observed compounds in the experiment. […]

PMCID: 5122192
PMID: 27933298
DOI: 10.3389/fmolb.2016.00077

[…] area of the chromatographic peak was calculated among replicate injections (n = 2). features were grouped into spectra, based on coelution and covariance parameters across the full dataset using ramclustr (broeckling et al., ). breifly, ramclustr groups several features derived from one compound (e.g., isotopes, adducts, fragments, multimers, etc) into a single unit, reducing analytical […]

PMCID: 5047709
PMID: 27729784
DOI: 10.2147/COPD.S107844

[…] three lockspray m/z measurements of protonated leucine-enkephalin were averaged and used to apply corrections to measured m/z values during the course of the analysis. the r software package ramclustr was used for analyte alignment and feature detection., samples (10 μl) for srm analysis were subjected to injection using an agilent autosampler with an analytical acquity uplc beh c18, 1.7 […]

PMCID: 4961386
PMID: 27459477
DOI: 10.1371/journal.pone.0159581

[…] on total signal and principal component 1 of principle component analysis, and the mean area of the chromatographic peak was calculated among replicate injections (n = 2). features were grouped with ramclustr [] and metabolites were annotated by matching retention index and mass spectra using nist v11 and v12, golm, metlin, and massbank metabolite databases. initial experiments indicated […]


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RAMClustR institution(s)
Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, USA; Department of Computer Science, Colorado State University, Fort Collins, CO, USA; Department of Biochemistry, Colorado State University, Fort Collins, CO, USA; Department of Stress- and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
RAMClustR funding source(s)
This tool was funded by the Fulbright Scholarship Program of the U.S. Department of State and the Higher Education Commission of the Government of Pakistan.

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