MetaboAnalyst

Update History:

Added support for enrichment analysis on ~3700 metabolomics pathways from RaMP in Enrichment Analysis module (11/09/2023);
Users can directly upload Metabolon data sheet in Statistics, Pathway, Enrichment, and Biomarker analysis modules (09/08/2023);
Enhanced support for metadata table integrity check based on user feedback from OmicsForum (08/18/2023);
Added a checkbox to allow users to explicitly specify group order in Data Editor (07/22/2023);
Enhanced error messages for data upload format check; fixed the issue with figure legend in 3D scatter plot (06/22/2023);
Enhanced result table download for mummichog and covariate adjustment analysis (04/30/2023);
Feature enhancement to improve performance and visualization for complex large data based on user feedback from OmicsForum (03/15/2023);
Enhanced linear models with covariate adjustments (Statistical Analysis [metadata table] module) to better support different study designs (02/13/2023);
Enhanced support for metadata table integrity check based on user feedback from OmicsForum (08/18/2023);
Fixed issues in SSP (single sample profiling) and SMPDB pathway view (07/30/2023);
Added a checkbox to allow users to explicitly specify group order in Data Editor (07/22/2023);
Enhanced error message for data upload format check; fixed the issue with figure legend in 3D scatter plot (06/22/2023);
Enhanced result table download for mummichog and covariate adjustment analysis (04/30/2023);
Minor bug fixes and feature enhancements based on user feedback from OmicsForum (04/06/2023);
Upgraded the interactive 3D scatter plot for PCA, PLSDA and sPLSDA visual exploration (03/19/2023);
Feature enhancement to improve performance and visualization for complex large data based on user feedback from OmicsForum (03/15/2023);
Enhanced linear models with covariate adjustments (Statistical Analysis [metadata table] module) to better support different study designs (02/13/2023);
Fixed minor issues and improved documentation based on user feedback from the MetaboAnalystR GitHub (11/08/2022);
Upgraded to Prime Faces 12.0.0; (10/12/2022);
Fixed an issue with mini-heatmap display in Sig. Feature view (Biomarker Module) (09/26/2022);
Enhanced enrichment analysis using reference metabolome for targeted metabolomics based on user feedback (09/09/2022);
Enhanced ANOVA to better support more complex design in Statistics (metadata table) module (09/02/2022);
Users can manually re-order groups for heatmap visualization in Statistics (one factor) module (08/29/2022)
Updated all tutorials based on the latest version (07/12/2022);
We are happy to introduce User Forum. Please use it for all queries and support related to MetaboAnalyst (06/14/2022);
Fixed the issue in plotting threshold line for t-test result (06/06/2022);
Enhanced error messages for metadata file upload (05/28/2022);
Upgraded R version to 4.1.3. Please let us know if you notice any functions stop working (05/14/2022);
Added options for adjusting font size and legend display in heatmap visualization (05/02/2022);
Fixed the legend issue for PCA pair plot (03/31/2022);
Updated the PDF report generation for the Statistical Analysis [metadata table] module (03/01/2022);
Added null check and error message when users forget to upload a file (03/25/2022);
Enhanced support for data containing empty columns and better error messages for time series analysis (01/28/2022);
Check out our updated documentation for MetaboAnalystR 3.2 release (12/20/2021);
Enhanced feature box plot visualization based on user feedback; (12/15/2021)
Upgraded the web framework to PrimeFaces v11; (12/10/2021)
Users can now perform partial correlation analysis in our Statistical Analysis [metadata table] module; (12/03/2021)
Enhanced volcano plot for download; users can now specify which features to label by clicking on the data points (12/03/2021);
Users can now download network view as as a high-resolution PNG image (12/01/2021);
Updated user traffic for the last five years (11/19/2021);
Some minor issue (DSPC) fixes, and feature enhancement for Biomarker Analysis Tester track (11/12/2021);
Enhanced results for Raw Spectra Processing module to enable more informative data exploration (10/06/2021);
Replaced the Venn Diagrams with interactive UpSet plots for summarizing meta-analysis results (10/01/2021);
Upgraded Two-Factor/Time-Series module to Statistical Analysis [metadata table] to support complex metadata in clinical, epidemiological or environmental studies (09/12/2021);
Joint-Pathway Analysis module now supports integrating untargeted metabolomics (peak list) with transcriptomics (gene list) for functional analysis (09/10/2021);
Comprehensive interface refactoring and enhancements (08/12/2021);
Code refactoring (meta-mummichog) and fixed missing value issue for functional enrichment analysis (08/09/2021);
Improved size calculation for heatmap visualization in Statistics module (08/05/2021);
Added support for VIP plot for Orthogonal Partial Least-Squares (OPLS) in Statistics module (07/15/2021);
Minor bug fixes based on user feedback (05/31/2021);
Improved functional meta-analysis data upload page for more flexible data processing (04/27/2021);
Fixed the issue with synchronized 3D scatter plots for scores and loadings (04/12/2021);
Fixed the issue for multi-group figure legend (04/06/2021);
Upgraded to Primefaces 10 (03/31/2021);
Minor bug fix and code refactoring for better performance (03/15/2021);
Added support for merging technical replicates with different mathematical models and QC measures (02/18/2021);
Updated KEGG IDs in internal compound databases (02/09/2021);
Enhanced name handling to better accommodate special characters in compound/lipid names (02/09/2021);
Fixed performance issue related to DSPC (02/01/2021);
Added seven tutorials introducing new features in MetaboAnalyst 5.0 (01/15/2021);
Users can perform meta-analysis of global metabolomics data as illustrated in our COVID-19 paper (01/09/2021);
Updated the KEGG global metabolic map for better metabolome coverage (01/08/2021);
Minor bug fixes and feature enhancements based on user feedback (01/06/2021);
Users can now enter Study IDs to analyze data deposited in the Metabolomics Workbench (12/20/2020);
Added a new module - Functional Meta-analysis to allow integrating global metabolomics data at pathway or peak levels (12/15/2020);
Users can Start New Journey from the Download page at the end of analysis session. (12/14/2020);
Expanded compound database for lipids (>150,000 lipids) together with a smart compound name matching algorithm (12/10/2020);
Upgraded main interactive plots; enhanced Enrichment module and Pathway Analysis module (12/07/2020);
Enhanced underlying compound database for lipids (>150 000 lipids now supported!) + implemented a smart compound name matching algorithm (12/10/2020);
Fixed volcano plot issue in large data analysis (11/30/2020);
Enhanced support for lipids (name mapping and metabolite set analysis) in the Enrichment Analysis module (11/24/2020);
Added interactive heatmaps support for Pathway Analysis to allow enrichment tests on any clustered features (11/18/2020);
Added support for Debiased Sparse Partial Correlation (DSPC) network analysis in Network Explorer module (10/15/2020);
Enhanced support for peak-table upload in MS Peaks to Paths (10/08/2020);
Updated internal compound database (10/08/2020);
Bug fix for KO-mapping in the Network Explorer Module (09/28/2020);
Added disease-associated fecal metabolite set to the Enrichment Analysis module (09/28/2020);
Enhanced pathway results table for MS Peaks to Paths (09/22/2020);
Minor bug fixes (heatmaps, enrichment analysis, etc) based on user feedback (09/17/2020);
Updated R from 3.6.2 to 4.0.2 (09/14/2020);
Fixed the ANOVA issue (09/07/2020);
Added 10 metabolite sets to the MS Peaks to Paths Module (08/28/2020);
Updated clustering graphics (k-means and SOM) (08/27/2020);
Added chemical class metabolite sets to the Enrichment Analysis module (08/24/2020);
Code refactoring and interface updates for better experience (08/17/2020);
MetaboAnalyst image now added to Docker Hub (08/05/2020);
Check out our new MS Spectra Processing module for optimized LC-MS spectra processing (07/03/2020);
Users can now click Details Table to directly update feature names for graphical display (07/02/2020);
Users can now use Graphics Center to specify colors and shapes for key images (07/02/2020);
The default missing values are now replaced by 1/5 of min positive values of their corresponding variables (06/29/2020);
Added a step-by-step tutorial for MetaboAnalystR 3.0 (05/08/2020); ;
Check out our MetaboAnalystR 3.0 featuring three key improvements for optimized global metabolomics (05/03/2020);
Users can now upload mzTab 2.0-M files to the Statistical Analysis module (04/22/2020);
Updated Java (from Java8 to Java11) and Primefaces (from PF7 to PF8) (04/08/2020);
Updated gene mapping database for integrative analysis (03/31/2020);
Fixed I/O issue for zip file upload (03/10/2020);
Users can now customize currency metabolites or adducts for Peaks to Pathway module (02/07/2020);
Fixed bug in specifying different colors using Image Options (01/08/2020);
Updated the KEGG pathway libraries for Peak to Pathway (mummichog) module (01/03/2020);
Enhanced I/O support for mummichog data upload; fixed log10 (instead of log) for visualization (12/18/2019);
Fixed broken links for network analysis (12/05/2019);
Fixed the name mapping issue (11/25/2019);
Fixed the issue with SVG export for 3D interactive PCA plot in time-series / two-factor analysis module (11/15/2019);
Both the database and algorithm are updated for Joint Pathway Analysis (11/11/2019);
Updated KEGG pathways for Pathway Analysis and Enrichment Analysis modules (10/30/2019);
Updated R from 3.5.1 to the latest version 3.6.1 (10/16/2019);
Our latest protocols on using MetaboAnalyst 4.0 is now available (09/21/2019);
Users can upload MS peak intensity tables and test enriched pathways for any peak cluster of interest (MS Peaks to Pathways) (09/13/2019);
Enhanced enrichment network view for metabolite set enrichment analysis (06/25/2019);
Added mixed mode support to allow combining peaks from both postive and negative ion modes (MS peaks to pathways) (06/10/2019);
Enhanced the summary plot for individual metabolite set in Enrichment Analysis module (04/23/2019);
Enhanced support for various input formats and added interactive result summary for MS Peaks to Pathways module (04/10/2019);
Added support for synchronized 3D visual exploration for PCA/PLS-DA scores and loading plots (04/07/2019);
Added support for the GSEA algorithm (MS Peaks to Pathways) (03/22/2019);
The download table in compound ID conversion now contains SMILES (03/15/2019);
Enhanced ID mapping for KEGG compounds (03/11/2019);
Enhanced KEGG pathway generation to address the occasional failure issue during peak time (01/24/2019);
Fixed the issue for compound view in Pathway Analysis module (01/07/2019);
Enhanced support for parsing data input and data editing (01/02/2019);
Updated Joint Pathway Analysis module to be consistent with Pathway Analysis (12/21/2018);
Fixed the issue with data filtering (12/18/2018);
Upgraded R to version 3.5.1 (12/12/2018);
Enhanced error handling for the Mummichog Analysis module (11/15/2018);
Upgraded to HTTPs for more secure communications (11/05/2018);
Enhanced graphics for scores and loadings plots in chemometrics methods (10/06/2018);
Enhanced visualization for SMPDB pathways (09/28/2018);
Minor interface enhancement based on user feedback (09/11/2018);
Fixed the issue with mummichog p value computing (08/03/2018);
Updated to Primefaces 6.2 (07/13/2018);
Fixed issue with name mapping in enrichment analysis (06/28/2018);
Fixed issue with pathway visualization (06/18/2018);
Enhanced pathway image generation to deal with concurrency issue (06/13/2018);
Fixed the issues for name mapping and node-click interactions in pathway visualization (06/12/2018);
Fixed the issue in the downloaded CSV file generated during name mapping (06/10/2018);
Fixed the issue for data editor in biomarker analysis (05/28/2018);
Fixed the issue for sample hold-out analysis in biomarker analysis (04/23/2018);
Fixed the issue with time-series group ordering based on numeric values (04/19/2018);
Enhanced support for SVG export for KEGG global network (04/04/2018);
Updated Resources on various local installation options including Docker (03/10/2018);
Minor bug fixes and feature enhancements based on user feedback (02/20/2018);
Updated tutorial and FAQs for the new modules (02/09/2018);
Release of MetaboAnalyst 4.0 togehter with a companion R package MetaboAnalystR. You can still access version 3.0 here (01/29/2018);
Updated interface for module selection (01/22/2018);
Updated compound libraries based on the lastest HMDB (v4.0) (01/18/2018);
Added a new module for network-based integrative analysis for metabolites, genes (including KEGG Orthologs from metagenomics studies) (01/12/2018);
Added a new module for meta-analysis for multiple metabolomics data sets for robust biomarker identification (01/08/2018);
Added a new module for pathway enrichment analysis for untargeted metabolomics (mummichog) (12/20/2017);
Minor bug fixes and interface improvements based on user feedback (12/20/2017);
Added support for interactive enrichment network and SVG export (12/15/2017);
Minor bug fixes and interface improvements based on user feedback (12/07/2017);
Enhanced PLS-DA for multiple-group analysis (10/13/2017);
Fixed the broken link for downloading MetaboAnalyst.war file (09/20/2017);
Fixed the issue for PLS-DA on paired samples (09/14/2017);
Enhanced support for Feature Selection for large data in Biomarker Tester (08/12/2017);
The downloaded correlation matrix is now synchronized with current clustering (08/07/2017);
Fixed the bug for computing ASCA permutation (07/27/2017);
Doubled the max allowed feature numbers for untargeted metabolomics (06/27/2017);
Updated random forest methods to control randomness (06/27/2017);
Fixed bug for ANOVA analysis for multiple groups when peak lists files are uploaded (06/15/2017);
Added support for heatmap generation on group averages and correlation analysis for either features or samples (06/10/2017);
Updated univariate analysis (ANOVA, t-tests, Volcano plot) for FDR-adjusted p values (05/12/2017);
Code refactoring for better peroformance (04/12/2017);
Added support for peak filtering based on QC samples for untargeted metabolomics (03/10/2017);
Added support for "flipping" PCA for cross-study comparison (02/09/2017);
Added support for network summary of enrichment analysis result (02/06/2017);
Fixed the bug in feature table display in Biomarker Tester module (01/05/2017);
Updated pathway result table to show all pathway compounds (with hits highlighted) (11/25/2016);
Improved Normalization and Data Editor for better user experience (11/15/2016);
Added support for sparse PLS-DA analysis (10/28/2016);
Minor bug fix and performance tuning (09/15/2016);
Fixed the issue for t-tests plotting (09/09/2016);
Added support for quantile normalization (08/29/2016);
Improved name mapping functions for common metabolite names (08/18/2016)
Joint-pathway analysis was back to work (08/01/2016)
Updated PCA to perform default data centering (07/28/2016)
Code refactoring to improve memory efficiency (07/20/2016)
More than 1 million jobs have been processed since 06/2015 (06/15/2016)
Updated Time Series module to support analysis of time-series only data (06/08/2016);
Added support for Orthogonal PLS-DA (05/16/2016);
Improved support for dealing with special characters and punctuations (05/11/2016);
Added support for batch effect correction for multiple data sets (Other Utilities module) (02/22/2016);
Upgraded the web framework for better performance (02/18/2016);
Updated the Google Cloud server for improved performance (10/30/2015);
Added support for detailed ROC curve analysis of individual biomakers (10/29/2015);
Several feature improvements and bug fixes based on user feedback (10/16/2015);
Added support for logistic regression in ROC Tester (08/12/2015);
Added support for computing compound ratios in biomarker analysis (08/03/2015);
Minor bug fixes and feature enhancements (data IO, PLS-DA, enrichment analysis) to deal with special cases in user inputs (07/20/2015);
Updated Multivariate Biomarker Analysis module with flexible interface and improved capacity for computing on large datasets (06/05/2015);
MetaboAnalyst now has its logo image (top right) (05/15/2015)
MetaboAnalyst 3.0 paper is now available on the 2015 NAR web server issue
Users can now specify symbols in the PCA/PLSDA scores plots (under Image options - previous Color picker) (04/20/2015)
The loading plots in PCA and PLS-DA are now clickable and zoomable (04/02/2015)
T-tests and ANOVA results, as well as volcano plot are now interactive and zoomable (03/31/2015)
Updated heatmaps to support both overview and high resolution details view (03/25/2015)
Users can now upload either tab delimited file (.txt) or csv file (03/20/2015)
Updated data filter to permit feature-specific normalization on low variance features (03/19/2015)
Updated dendrogram for better visualization and minor bug fixes (03/14/2015)
Bug fixes for feature-specific normalization and fold changes analysis (03/13/2015)
Minor bug fixes for two factor and time-series data analysis (03/04/2015)
Enhanced support on building biomarker models for predicting new samples under ROC Tester (02/06/2015);
Updated the confidence interval graphics for PCA, PLSDA and ROC curves; (01/06/2015)
Updated the Heatmaps function for better visualization of large data; (12/22/2014)
Added a new module for Integrated Pathway Analysis on genes and metabolites that have changed significantly under the same experimental conditions; (12/17/2014)
Added a new module for Biomarker Analysis; (12/12/2014)
Added sorting and filtering support in the feature details table; (11/12/2014)
Fixed a bug on broken functions after missing value imputation; (11/10/2014)
PCA and PLSDA 3D plots now are interactive; (10/31/2014)
A new module (Power Analysis) is added to support sample size and power analysis for pilot metabolomic studies; (10/30/2014)
Added Compound ID conversion support (under Other Utilities); (10/24/2014)
Added support for uploading custom metabolite sets and custom metabolome in Enrichment and Pathway analyses; (10/20/2014)
Fixed the dialog issue in compound name mapping; (10/17/2014)
Added support for labeling PCA/PLSDA loadings plot; (10/09/2014)
Added pathway analysis support for Schistosoma mansoni, Malaria, Trypanosoma brucei and Synechococcus elongatus; (09/30/2014)
Updated compound name mapping algorithm for improved performance; (09/29/2014)
Updated compound and pathway IDs based on the latest HMDB and SMPDB; (09/12/2014)
Users can now edit or re-order groups under Data Editor page; (08/26/2014)
Updated FAQs for recent changes; (08/08/2014)
Added a new tutorial on raw spectra processing using XCMS for MetaboAnalyst; (08/04/2014)
Completely upgraded the web application framework for better performance and user experience; (07/28/2014)
Fixed color reversing issue with PLS-DA VIP plot; (07/15/2014)
Updated two-way ANOVA for repeated measures; (06/05/2014)
Updated VIP plot for supporting black and white colors; (02/05/2014)
Added nonparametric version for t-tests and ANOVA, and minor bug fix; (02/22/2013)
Added support for heatmaps on grayscale; added link to download the underlying matrix for correlation heatmaps. (08/25/2012)
Presentation at the 8th Metabolomics Conference at Washington DC is available under Tutorial; (07/04/2012)
Updated Data Filtering and Data Normalization procedures; (07/03/2012)
Updated compound database; (06/22/2012)
Updated correlation heatmap analysis; (05/27/2012)
Pathway analysis now supports Mesorhizobium loti and Gallus gallus (chicken); (05/10/2012)
Minor bug fix and updates; (03/29/2012)
Pathway analysis now supports Gallus gallus (chicken); (03/18/2012)
Fixed missing link to high-resolution images generated for pathways. (03/03/2012)
Updated correlation heatmaps and some minor bug fixes. (02/16/2012)
Minor update and bug fix; (01/05/2012)
Added a new module for data quality check - available at QC and Other Utilities tab on the data upload page(01/02/2012);
All important images can be reproduced in high resolution (150/300/600 DPI) in PNG, TIFF, PostScript, SVG, or PDF format. Just click the above each image! (12/31/2011);
Updated Bioconductor to the latest version (2.9) and performed compatibility tests(12/17/2011);
Upgraded R to the latest version (2.14.0) and some visual enhancement (11/26/2011);
Added correlation heatmap visualization feature (under correlation node, 10/08/2011);
Enhanced support for univariate analysis and minor bug fixes (09/14/2011);
Minor bug fixes and some visual improvements (08/10/2011);
Updated graphical output for PLS-DA VIP plot (07/23/2011);
Minor bug fixes and some visual improvements (06/23/2011);
Added a new module for two-factor and time-series data analysis (05/12/2011);
MetaboAnalyst is featured on Nature Protocols (05/10/2011)
Enhanced support for Heatmap generation (03/03/2011);
Added two normalization methods - normalization to sample median and quantile normalization based on recent publications (02/26/2011);
Added an Outlier detection tab for data analysis using Random Forest (02/08/2011);
Added a Color picker (under Processing node) for setting colors for figures (02/07/2011);
Fixed several broken functions based on user feedback (02/06/2011);
Improved message output and minor bug fix due to some package updates (02/02/2011);
Added a Data filter function for large data with many noisy features (02/02/2011);
All significant features are now available as text files in the Download page (02/01/2011);
Fixed the issue with reading CSV files generated by Miscrosoft Excel (12/6/2010);
MetaboAnalyst server has been upgraded, let us know if you experience any problems (12/5/2010);
PLS-DA now calculates R² and Q² values in the Cross Validation section. (09/28/2010);
Upgraded unzip function to better support files created with WinZip (09/27/2010);
Fixed the image update issue associated with the new server (09/18/2010);
MetaboAnalyst is now hosted on a dedicated new, powerful server (09/12/2010);
Added support for applying a reference metabolome for enrichment analysis and pathway analysis. (09/08/2010);
Added Correlation Analysis to identify significant features with patterns of interests (09/05/2010);
MetaboAnalyst now supports metabolite set enrichment analysis and pathway analysis (09/01/2010);
Updated the error tracking system (07/18/2010);
High resolution (300 dpi) images are available for score or loadings plots from PCA and PLSDA analysis (07/17/2010);
PLSDA permutation test now supports multi-group data (07/14/2010);
Updated the pathway library to use SMPDB (07/13/2010);
Improved 3D visualization for PCA and PLSDA results (07/12/2010);
MetaboAnalyst was presented on the the Metabolomics Conference 2010 (Amsterdam, The Netherlands) (download slides)(07/09/2010);
Fixed the data upload problem encountered for transposed data (samples in columns, features in rows) and for paired comparison (07/07/2010) ;
Bug fix: Color inconsistencies b/w the confidence ellipses and sample class labels (used in PCA abd PLS-DA 2D plot)(06/17/2010) ;
Updated the interface for zip file upload to support multiple-group analysis of peak lists and spectra data (06/15/2010) ;
Introducing Data Editor to support samples/features exclusion (i.e. outliers) during analysis (06/14/2010) ;
Updated documentations and reports for multi-group analysis (06/11/2010) ;
Added a new function - Analysis of Variance (ANOVA) and associated post-hoc methods for multi-group analysis (06/10/2010) ;
Enhanced PLS-DA support for multi-group analysis (06/05/2010);
MetaboAnalyst now supports data analysis for more than two groups. (06/01/2010);
For data collected from human or other mammalian species, you may also want to visit our new web application MSEA (http://www.msea.ca) for more advanced data analysis. (05/11/2010);
Improved graphics for PCA and PLSDA result (03/21/2010);
MetaboAnalyst is now hosted on a new and powerful server (01/31/2010);
Fixed t-tests errors on constant values (01/31/2010);
Added functions to plot 2D confidence regions for PCA and PLS-DA scores plots (12/12/2009);
MetaboAnalyst tutorial presented on the Metabolomics Conference 2009 (Edmonton, Canada) (download slides)(09/12/2009);
MetaboAnalyst is now hosted on Tomcat (02/06/2009);
PLS-DA now provides p value based on permutations (20/05/2009);
Integrity check added for sample/feature names (28/05/2009);
High-resolution images for heatmap and dendrogram are available (15/05/2009);
Improved function for unzipping compressed data (.zip) (10/05/2009);