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Protocols

MSClust specifications

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Unique identifier OMICS_01954
Name MSClust
Alternative name Multi-Seeds based Clustering algorithm
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

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Publication for Multi-Seeds based Clustering algorithm

MSClust citations

 (27)
call_split

Comprehensive untargeted metabolomics of Lychnnophorinae subtribe (Asteraceae: Vernonieae) in a phylogenetic context

2018
PLoS One
PMCID: 5764248
PMID: 29324799
DOI: 10.1371/journal.pone.0190104
call_split See protocol

[…] d 36,861 and 24,482 mass signals in both positive and negative electrospray ionization mode (UHPLC-MS), respectively, at ion intensity higher than 105. Mass signals were subsequently re-grouped using MSClust (Netherlands Genomics Initiative/Netherlands Organization for Scientific Research) [], resulting in 73 (GC-MS), 2,972 (UHPLC-MS negative ionization mode) and 2,974 (UHPLC-MS positive ionizatio […]

library_books

Metabolomic analysis of tomato seed germination

2017
Metabolomics
PMCID: 5653705
PMID: 29104520
DOI: 10.1007/s11306-017-1284-x

[…] less than three RILs or lower than 35 were discarded. Remaining peaks below background were randomized from 50 to 100%. Out of all the remaining mass signals (5601), centrotypes were formed using the MSclust program (Tikunov et al. ) with the following parameters: correlation threshold at 0.9 with 0.01 margin softness; PDF correlation of 0.8 with margin of 0.02; a peak width of 20 with a margin of […]

library_books

Metabolite profiling and associated gene expression reveal two metabolic shifts during the seed to seedling transition in Arabidopsis thaliana

2017
Plant Mol Biol
PMCID: 5688192
PMID: 29046998
DOI: 10.1007/s11103-017-0665-x

[…] co®), and further baseline correction, accurate mass calculation, data smoothing and noise reduction, followed by alignment between chromatograms were performed using the MetAlign software (Lommen ). MSClust was used to remove metabolite signal redundancy in aligned mass peaks tables and to retrieve mass spectral information of metabolites using mass peak clustering (Tikunov et al. ). The mass spe […]

library_books

From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

2017
GigaScience
PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] CAMERA or by the ALLocatorSD algorithm, which is optimized for dealing with the particularities of 13C labeled data by grouping mirrored isotopes (lighter isotopologues 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 […]

call_split

Untargeted metabolomic analysis of tomato pollen development and heat stress response

2017
PMCID: 5486769
PMID: 28508929
DOI: 10.1007/s00497-017-0301-6
call_split See protocol

[…] eak signal was subtracted to the estimated noise signal. Compound mass spectra and quantitative ions were extracted from the modified MetAlign outputs using a method described in Tikunov et al. () by MSClust software (available from www.metalign.nl). MSClust output was reduced by keeping compounds that were quantitatively present in all the replicates of one of the experimental treatments: heat st […]

library_books

Metabolomic homeostasis shifts after callus formation and shoot regeneration in tomato

2017
PLoS One
PMCID: 5421760
PMID: 28481937
DOI: 10.1371/journal.pone.0176978

[…] The NetCDF files were obtained from ChromaTOF software 4.50.8.0 chromatography version (LECO Corporation, USA) GC-MS were further analysed using MetAlign 3.0 (www.metalign.nl) [] and MSClust [] software with a signal to noise ratio of ≥ 2, for baseline correction, noise estimation, alignment and extraction of ionwise mass signal. The mass signals that were present in <3 samples we […]


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MSClust institution(s)
College of Automation, Northwestern Polytechnical University, XI'an, China; Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA; Keck Biotechnology Laboratory, Biostatistics Resource, Yale School of Medicine, New Haven, CT, USA
MSClust funding source(s)
This work was supported in part by NIH GM59507, UL1 RR024139, National Natural Science Foundation of China (No. 61170134), Aeronautical Science Foundation of China (No.20100853010) and Doctorate Foundation of Northwestern Polytechnical University (No. cx201017).

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