An extensible web component that can be easily integrated in current web applications and databases, providing NMR processing and visualization functionalities. NMRPro is highly extensible to include new functionalities according to the needs of each application. It integrates server-side processing with client-side interactive visualization through three parts: a python package to efficiently process large NMR datasets on the server-side, a Django App managing server-client interaction, and SpecdrawJS for client-side interactive visualization.
An open mark-up language for NMR data. nmrML is currently under heavy development and is not yet ready for public use. The development of this standard is coordinated by Workpackage 2 of the COSMOS - COordination Of Standards In MetabOlomicS Project. COSMOS is a global effort to enable free and open sharing of metabolomics data.
A combined chemoinformatic approach for objective and systematic analysis of untargeted 1H NMR-based metabolic profiles in quantitative genetic contexts. The R/Bioconductor mQTL.NMR package was designed to (i) perform a series of preprocessing steps restoring spectral dependency in collinear NMR data sets to reduce the multiple testing burden, (ii) carry out robust and accurate metabotype quantitative trait locus (mQTL) mapping in human cohorts as well as in rodent models, (iii) statistically enhance structural assignment of genetically determined metabolites, and (iv) illustrate results with a series of visualization tools. Built-in flexibility and implementation in the powerful R/Bioconductor framework allow key preprocessing steps such as peak alignment, normalization, or dimensionality reduction to be tailored to specific problems.
Provides an interface for process, analyze and visualize 1D and 2D nuclear magnetic resonance (NMR) data. MatNMR is an extendable open source software which includes several modules that allows users to run various analysis such as spectral deconvolution or quadrupolar tensor fitting. Besides, it offers a viewer for 2D data providing 2D and 3D contour, surface and line plots in a wide range of formats and standards.
Assists users for metabolomics data analysis. Specmine includes a workflow that can be adapted for specific case studies, addressing tasks as data loading, pre-processing, normalization, metabolite identification, univariate and multivariate statistical analysis, clustering, machine learning and feature selection. It also offers modules for the visualization of data including box plots, volcano plots and spectra.
Identifies metabolites in H-NMR spectra of complex mixtures. MetaboHunter is a web-server application based on two manually curated reference libraries. The software provides three distinct methods: (i) a scoring function, (ii) an iterative greedy selective approach and, (iii) selection approaches with a user adjustable chemical peak drift parameter. There are 4 functional views: (i) a Processing View, (ii) a Search Results View, (iii) a Plot View and, (iv) a Peaks Hit Map view.
Analyses advanced time-domain of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) data. jMRUI can significantly help the user to track the processing history performed on data. The approach offers basic processing tracking and is not suitable for complex data processing and extensive studies. It helps to better organize the processing history and increases the reproducibility and documentability of all spectroscopic processing.
Assists the spectroscopist in making decisions. XEASY permits to support the analysis of nuclear magnetic resonance (NMR) spectra for three-dimensional structure determination of biological macromolecules. It was developed for working with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra.
Assists users for the chemometric analysis of nuclear magnetic resonance (NMR), infrared (IR) or Raman spectroscopy data. ChemoSpec is an R package that includes modules to plot and inspect spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA) and model-based clustering. This method was designed with metabolomics data sets in mind.
An interactive 1D NMR spectra processing tool dedicated to metabolomics. The NMRProcFlow open source software provides a complete set of tools for processing and visualization of 1D NMR data, the whole within an interactive interface based on a spectra visualization.
Permits users to view and analyze processed Nuclear Magnetic Resonance (NMR) data in multiple, canvas windows with correlated crosshairs and rich annotations. NMRViewJ is a graphic application for visualization and analysis of macromolecular NMR software that proposes advanced analysis tools. This tool facilitates assignments of macromolecular NMR spectra and analysis of datasets used in experiments like relaxation and titration analysis.