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Update History

  • Code refactoring for improved performance (01/23/2026);
  • Fix the for datasets selection issue for correlation analysis (12/2025);
  • Supports projection of statistically significant features from differential analysis, paired features from correlation analysis, and top-ranked features from multi-omics integration methods into the network integration module (12/2025);
  • Enables direct projection of correlation analysis results into the mediation analysis (12/2025);
  • Fix the network display issue (12/2025);
  • Add Mediation analysis (12/2025);
  • Added a network integration module enabling direct input of feature lists for functional exploration (11/2025);
  • Updated to the new OmicsAnalyst 2.0 framework and interface (11/2025);
  • Updated the default clustering exploration from hierarchical clustering to k-means to be consistent (01/07/2025);
  • Enhanced error message(01/05/2025);
  • Enhance Limma for significant feature identification (12/015/2024);
  • Add Differential network (12/012/2024);
  • Add Pairwise Linear model (12/10/2024);
  • Add Chord diagram (12/08/2024);
  • Add biplot (12/06/2024);
  • Add Multivaraite Biomarker Modeling (12/04/2024);
  • Add Univariate Biomarker Modeling (12/02/2024);
  • Add Variance Decomposition for individual dataset exploration (11/29/2024);
  • Add the metadata explorer (11/25/2024);
  • Harmonize the interface to add new analysis tracks (11/20/2024);
  • Upgraded Java 17 to Java 21 (11/15/2024);
  • Migrated from Java EE to Jakarta EE (09/21/2024);
  • Fix an issue for meta-data parsing (07/29/2024);
  • Code refactoring for better performance (04/29/2024);
  • Upgraded to R 4.3.2, Java 17, and PrimeFaces 13.0.7 (12/20/2023);
  • Fixed the null issue in correlation network analysis when two matrices share the same feature ID (10/20/2023);
  • Enhanced support to adjust circle size in network visualization (10/15/2023);
  • R code cleaning and refactoring to prepare for the upgrade (10/10/2023);
  • Minor text updates and interface improvements (08/18/2023)
  • Added a new example containing 3 omics types (07/15/2023);
  • Bug fix for graphml export in 2d network and SVG download (05/25/2023);
  • Bug fix MOFA2 loading table display (04/20/2023);
  • Enhanced data upload page to allow more flexible multiomics data upload (03/15/2023);
  • Bug fix for highlighting groups in 3D scatter plot (02/15/2023);
  • Enhanced support for coloring and shapes for Procrustes Analysis (01/13/2023);
  • Upgraded to PrimeFaces 12.0.0; Home page enhancement (10/15/2022);
  • Code refactoring and minor feature enhancements (07/05/2022);
  • Enhanced support for metabolomics and microbiome data integration by highlighting those overlap with GEM potential metabolites (06/14/2022);
  • Bug fixes for missing values imputation and error messages (06/01/2022);
  • Users can now specify custom features for correlation network creation (01/17/2022);
  • Upgraded the web framework to the PrimeFaces 11.0 (12/10/2021);
  • Added support for downloading correlation pairs in correlation network (12/10/2021);
  • Bug fix for png generations, heatmap and network for unannotated input matrices (09/30/2021);
  • Fixed the issue with DIABLO feature vector display and enrichment analysis in biplot (06/28/2021);
  • Added cookie consent form to allow disable tracking user traffic based on Google Analytics (04/19/2021);
  • Minor bug fixes for 3D scatter plots and updated documentations (04/15/2021);
  • Added a case study based on human pregnancy multi-omics data (proteomics and metabolomics) (04/05/2021);
  • Enhanced normalization for multi-omics integration (04/03/2021);
  • Add an option to ask users need to specify the Data Type (raw counts or continuous values) for each omics for better normalization and differential analysis (04/02/2021);
  • Interface updates for better user experience (04/02/2021);
  • Upgraded to PrimeFaces version 10 (03/31/2021);
  • Code refactoring for better performance (03/25/2021);
  • Added support to compute only between-omics correlation for more focused analysis (03/23/2021);
  • Added support for missing value estimation in omics data processing (03/18/2021);
  • Added detailed descriptions for all main methods upon user selection (03/06/2021);
  • Added support for biplot ellipsoid and contour option for 3D scatter plot visualization (02/26/2021);
  • Code refactoring to reduce memory footprint and data I/O (02/15/2021);
  • Added Analysis Overview &Customization page to display key result and diagnostic plots for all methods (01/23/2021);
  • Fixed the heatmap synchronization issue and added support for color-blind friendly palette (01/11/2021);
  • Improved documentations (updated FAQs and added video tutorials) (12/20/2020);
  • Added a Gallery page to showcase several key graphical capacities (12/08/2020);
  • Code refactoring and interface updates (11/20/2020);
  • Interface changes to the method selection page to expose more parameters (11/16/2020);
  • Added supported for partial correlation (11/12/2020);
  • Added support for PLS, rCCA algorithms(10/15/2020);
  • Added "Quality Check" page (09/20/2020);
  • Added support for DIABLO algorithm (09/11/2020);
  • New data upload interface (08/25/2020);
  • Implemented dual-heatmap viewer (08/09/2020);
  • Added enrichment analysis for metabolites (07/28/2020);
  • Users can perform targeted analysis on selected meta-data group or cluster (07/25/2020);
  • Added support for metabolic enrichment analysis (06/20/2020);
  • Added support for miRNA enrichment analysis (06/12/2020);
  • Implemented additional graph layout options for different use cases (04/29/2020);
  • Added support for miRNA upload (04/20/2020);
  • Implemented dual-heatmap viewer (04/05/2020);
  • Implemented network viewer, added supported for univariate correlation (03/25/2020);
  • Added support for animation view (01/20/2020);
  • Added non-parametric tests, limma, DEseq2, EdgeR for comparative analysis (01/18/2020);
  • Users can now highlight edges connecting omics sample pairs in integrative analysis; (01/15/2020);
  • Code refactoring and interface updates (01/10/2020);
  • Improved zooming effect (updating distances instead of size) (01/05/2020);
  • Added support for clustering within meta-data groups (01/02/2020);
  • Enhanced node rendering for better visual experience (12/31/2019);
  • Added tutorials - overview of OmicsAnalyst and multi-omics case-study (12/23/2019);
  • Users can now switch the content between the main view and inset view (12/18/2019);
  • Updated the gene annotation libraries based on the lastest NCBI and UniProt (12/16/2019);
  • Improved the color schemes based on ggplots for better visual experience (12/10/2019);
  • Added three new example datasets for testing and use case studies (12/05/2019);
  • Users can now customize the floor and background colors of the 3D environment (12/01/2019);
  • Code cleaning and refactoring (11/22/2019);
  • Added support for synchronized view for both sample space and feature space (11/15/2019);
  • Added support for Procrustes Analysis for integrative visualization of two omics data sets (11/10/2019);
  • Added an option for "explosive view" to further seperate clusters for better visual exploration (11/01/2019)
  • Added support for plotting ellipsoid around each cluster (10/25/2019);
  • Users now can double click the contour to select the corresponding clusters for comparative analysis (10/12/2019);
  • Added "contours" on the detected clusters (10/03/2019);
  • Added support for Density Peak Clustering (DPC) algorithm for discerning clusters of data points (09/28/2019)
  • Added support for shading effect for data points (09/21/2019)
  • Interface updates and code cleaning (09/15/2019)
  • OmicsAnalyst website setup (08/20/2019)
  • Improved performance for visualizing ~10,000 of data points (07/24/2019)
  • First prototype of 3D scatter plot with WebGL (07/01/2019)