MetaboNexus

- Deprecated

Website

https://www.sph.nus.edu.sg/index.php/research-services/research-centres/ceohr/metabonexus

Description

This provides a platform for preprocessing, annotation and metabolite identification. It is 'available' both online and to download. R Packages used in MetaboNexus include: plsdepot, rgl, randomForest, xml, gplots, xcms, snow, preprocessCore and caret. Data is first pre-processed with xcms and detected peaks can optionally be filtered if they are not present in a user-specified percentage of samples. Data can then be normalised to internal standards or quantile normalisation is available. Data can also be entered as a peaklist and then further analysed. Data can be transformed using: log10, log2 or loge transformation. Missing/zero values are replaced with half the minimum non-zero value of the dataset. Multivariate analysis is then performed: PCA (NIPALS), PLS-DA and random forest are offered. Univariate analysis offered includes: ANOVA, t-tests, Mann-Whitney U and Kruskal-Wallis. Users can identify adducts and then non-charged molecule is then searched for in a database: HMDB and METLIN. There is also a direct link to KEGG for pathway visualisation. Data can also be visualised with heatmaps.

Functionality

• Workflow

Instrument Data Type

• MS/LC-MS

Approaches

• Metabolomics/Untargeted

Computer Skills

Advanced

Software Type

• Web App
• Pipeline

Interface

• Web user interface
• Gaphical user interface

Operating System (OS)

Windows XP/Vista/7/8

Language

R

Dependencies

N/A

Input Formats - Open

mzData, mzXML, netCDF, Peaklist

Input Formats - Proprietary

N/A

Published

2014

Last Updated

2014

License

GPL

Paper

http://link.springer.com/article/10.1007%2Fs11306-014-0648-8