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Table 1 Qualitative assessment of metaX compared to other existing metabolomics tools

From: metaX: a flexible and comprehensive software for processing metabolomics data

No. 1 2 3 4 5 6 7 8 9 14 15 10 11 12 13 14
Feature metaX MAIT Workflow4Metabolomics MetMSLine metaMS MetaboNexus MetaboAnalyst XCMSOnline MeltDB Mzmine Mzmatch apLCMS EigenMS Metab Metabomxtr Metabolomics
Year 2015 2014 2014 2013 2013 2014 2009 2012 2008 2006 2011 2009 2014 2011 2014 2014
Language R, Java R R, Perl, Python, Java R R R R, Java R perl, JavaScript and R JAVA JAVA, R R R R R R
Platform independent Windows only √(windows & MacOS)
Open source project- and user-specific access
Usable offline - -
Power analysis - - - - - - - - - - - - - -
Automatic outlier samples finding - - - - - - - - - - - - -
PCA - - - - - -
Cluster analysis - - - - - - -
PLS-DA - - - - - - - - - -
ROC analysis - - - - - - - - - - - - -
Normalization Sum, PQN, VSN, QC-RSC, ComBat, SVR, quantiles - Linear or local polynomial regression fitting QC-LSC - Internal standard or quantile normalization Normalized by sum/median, Normalized by reference sample/feature, sample specific normalization and quantile normalization - Normalized by specific compound or feature Linear normalizaiton, normalized by internal standards Normalized by Reference sample - combination of ANOVA and singular value decomposition internal standard, medium, biomass(divides the intensity of each metabolite in a specific sample by the value of the biomass measured for this specific sample) normalized using a mixture model with batch-specific thresholds and run order correction normalized by sum,mean or media of each sample;normalized by specific reference;normalized by internal standards or optimal selection of multiple internal standards;
Biomarker analysis - - - - - - - - - - - - -
Correlation network analysis - - - - - - - - - - - - - - -
Metabolite identification - - - - -
Functional analysis - - - - - - - - - - - -
Quality assessment - - - - - - - - - - - - -
Peak picking - - - - -
HTML-Based report - - - - - (PDF) - (PDF) - - - - - - -