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BQuant specifications

Information


Unique identifier OMICS_13683
Name BQuant
Alternative name Bayesian Quantification
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0
Stability Beta
Requirements
mgcv, tmvtnorm, mvtnorm, Matrix, matrixcalc, MCMCpack, RColorBrewer
Maintained Yes

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Documentation


Maintainer


  • person_outline Cheng Zheng

Publication for Bayesian Quantification

BQuant citations

 (5)
library_books

On the stochastic phase stability of Ti2AlC Cr2AlC

2017
Sci Rep
PMCID: 5506059
PMID: 28698619
DOI: 10.1038/s41598-017-05463-1

[…] To account for the errors of assessed energies and their propagations to phase equilibria of the system, Bayesian quantification of model uncertainty were implemented. For this, prior and likelihood were assumed to be uniform and Gaussian distributions, respectively. The range of the uniform distribution […]

library_books

Bquant – Novel script for batch quantification of LCMS data

2016
PMCID: 5040634
PMID: 27709068
DOI: 10.1016/j.mex.2016.09.001

[…] Mass spectra processing is not performed by Bquant script. Component peak identification and integration have to be executed using instrument vendor software. All instrument control software performs these basic operations. Signals used for qua […]

library_books

Metabolomics Insights Into Pathophysiological Mechanisms of Interstitial Cystitis

2014
PMCID: 4180160
PMID: 25279237
DOI: 10.5213/inj.2014.18.3.106

[…] abolomics datasets, which include XCMS, MZmine, MetAlign, MathDAMP, and LCMStats. For NMR data analysis, the significantly altered NMR peaks can be identified by using a probabilistic approach called Bayesian Quantification (BQuant) [], which will allow the identification and quantification of metabolites in local regions of the 1H-NMR spectra. For preprocessing of data from MS-based metabolomics […]

library_books

Methodological approaches to help unravel the intracellular metabolome of Bacillus subtilis

2013
Microb Cell Fact
PMCID: 3722095
PMID: 23844891
DOI: 10.1186/1475-2859-12-69

[…] eported. In addition, new convenient tools for data analysis and visualization have been developed, such as mzMINE [,] and XCMS for MS data []; GAVIN [] and Metab [] for GC-MS analysis; BATMAN [] and BQuant [] for NMR analysis as well as, MetAssimulo [] and MBRole [], MetExplore [] and MSEA [] to handle and visualize data sets of increasing size.Sampling and pre-analysis represent the first steps […]

library_books

Gene network reconstruction from transcriptional dynamics under kinetic model uncertainty: a case for the second derivative

2009
Bioinformatics
PMCID: 2654806
PMID: 19218351
DOI: 10.1093/bioinformatics/btp028

[…] to find a set of predictive sub-models, we could proceed by stochastic search through the restricted sub-model space (see Casella and Moreno, ) or perhaps by conventional stepwise selection. However, Bayesian quantification of network uncertainty instead requires the computation of P(αij=1|y).In the simplest situation, one regulating gene dominates all others and expression measurements are availa […]

Citations

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BQuant institution(s)
Department of Statistics, Purdue University, West Lafayette, IN, USA; Fred Hutchinson Cancer Research Center, Seattle, WA, USA; School of Medicine, Department of Pediatrics, Indiana University, Indianapolis, IN, USA; Department of Chemistry, Purdue University, West Lafayette, IN, USA; Department of Computer Science, Purdue University, West Lafayette, IN, USA
BQuant funding source(s)
This work was supported by National Institutes of Health (NIH) (grants R01GM085291, 5K23RR019540 and UL1RR025761); Indiana University Signature Center Initiative; Indiana 21st Century Research & Technology Fund; Bisland Dissertation Fellowship from Purdue University.

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