Update History
  • Added ANCOM-BC2 for compositional-aware differential abundance analysis in both single-factor and multi-factor (covariate-adjusted) comparisons (09/21/2026);
  • Code refactoring and enhanced taxonomy database name mapping (09/21/2026);
  • Added a Food matrix category to Taxon Set Enrichment Analysis at mixed, species and strain levels (308 / 145 / 78 sets) to help tell food-derived microbes from host residents (09/21/2026);
  • Expanded the host-diet/lifestyle taxon sets, and extended the TSEA name-mapping table so that all library members can be matched (09/21/2026);
  • Integrated BugSigDB curated human gut signatures into the Taxon Set Enrichment Analysis libraries as ~1,400 study-specific taxon sets (plus 552 species-level sets) across disease, diet/lifestyle and medication categories (09/20/2026);
  • Fixed the LEfSe highlighting issue when only threshold update without result table update (04/27/2026);
  • Fixed the library loading (network and 3D scatter plot visualization) issue due to recent security policy updates (04/14/2026);
  • Added MOFA (Multi-Omics Factor Analysis) to support integrating microbiome and metabolomics data in the Microbial Metabolomics module (03/21/2026);
  • Added support for Aitchison distance measure in Beta Diversity analysis (03/18/2026);
  • Added support for Gini Index important measure in Random Forests (03/18/2026);
  • Added Faith's phylogenetic diversity (PD) as an alpha diversity metric (03/05/2026);
  • Added LinDA for compositional-aware differential abundance analysis in multi-factor models (03/05/2026);
  • Fixed phylogenetic tree-tip mismatch that could occur when feature names are modified during data processing (03/05/2026);
  • Fixed sample filtering and group selection errors in Marker Data Profiling (03/05/2026);
  • Fixed the issue for core microbiome computing and heatmap visualization based on an experimental factor (02/22/2026);
  • Code refactoring for improved performance (01/23/2026);
  • Upgraded R to the latest version 4.5.2 "[Not] Part in a Rumble" (12/15/2025);
  • Resolved a bug where the phylum level contained only a single unique taxon (11/17/2025);
  • Fixed the issue with interactive stacked bar/area plot (11/01/2025);
  • Code refactoring for improved memory efficiency (10/16/2025);
  • Fixed the issue for boxplot for Random Forests (09/14/2025);
  • Enhanced data format checking in user data upload (08/08/2025);
  • Improved integrity checking between feature names and phylogenetic tree labels (05/15/2025);
  • Fixed example data file and improved error messages for meta-analysis module (03/21/2025);
  • Enhanced functions for data upload support and error messages (02/21/2025);
  • Bug fix and improved error message for predicting microbial taxa associated with metabolites (01/13/2025);
  • Improved parser to deal with special characters in metadata and enhanced biplot (12/03/2024);
  • Updated support to allow users to specify the minimum value for data rarefying in normalization (11/01/2024);
  • Improved visualization support for core microbiome analysis (10/25/2024);
  • Upgraded to PrimeFaces 13.0.10 and Jakarta EE 10 framework (09/21/2024);
  • Enhanced documentations for normalization and single-factor analysis (07/31/2024);
  • Added support for viewing group averages in heatmap visualization (07/24/2024);
  • Added support for PCA option in beta-diversity visual exploration (07/18/2024);
  • Added support for Hutcheson's t-test for pairwise test in alpha diversity (07/02/2024);
  • Enhanced feature plots and interactive 3D scatter plot (05/24/2024);
  • Added options to allow users to control basic data filtering (04/15/2024);
  • Added support to allow users to rarefy to specific depth during data normalization (04/05/2024);
  • Added more informative error messages for data upload for MMP module and enhanced KEGG network visualization (03/05/2024);
  • Users can now choose either violin plot or box plot to view feature abundance profile (03/04/2024);
  • Added interactive Manhattan plot support for summarizing single-factor analysis results (03/01/2024);
  • Feature enhancements based on user feedback (02/15/2024);
  • Fixed the issue with PERMANOVA result display and improved error message for metadata integrity (01/29/2024);
  • Fixed the broken functions with Procrustes Analysis and DIABLO in MMP module (01/12/2024);
  • Fixed the SVG and PDF export issue related to Taxa Abundance Bar plot (01/03/2024);
  • Upgraded to the latest R 4.3.2 and PrimeFaces 13.0.1. (12/20/2023);
  • Enhanced support for raw sequence data upload based on user feedback (12/04/2023);
  • Enhanced rarefaction curve analysis and added more informative error message (11/16/2023);
  • Fixed the broken 3D scatter plot in meta-analysis module (11/16/2023);
  • Added support for 4 different models (LM, CPLM, NEGBIN, ZINB) for multi-factor analysis using MaAsLin2 based on user feedback (11/10/2023);
  • Fixed the issue for group name parsing and feature enhancements based on user feedback (10/25/2023);
  • Fixed issue with extra padding space when converting numeric to character for display (09/25/2023);
  • Added support for post-hoc pairwise comparison in Alpha Diversity Profiling method (08/25/2023);
  • Enhanced support for Heat Tree visualization based on user feedback from OmicsForum (08/18/2023); (08/18/2023);
  • Added support for pairwise PERMANOVA in Beta Diversity Profiling method (08/04/2023);
  • Our latest paper on MicrobiomeAnalyst 2.0 is now available on Nucleic Acids Research (05/11/2023);
  • Enhanced support for different view options of metabolic network (05/02/2023);
  • Improved contextual support and added PDF report generation for new modules (04/14/2023);
  • Fixed the issue with the direction calculation in LEfSe (04/11/2023);
  • Updated home page and tutorials; added new test datasets (03/15/2023);
  • Updated 3D scatter plots; code cleaning and minor bug fixes (03/10/2023);
  • Updated KEGG pathways and KOs databases (02/22/2023);
  • Consolidated the Taxon Set libraries (02/15/2023);
  • Added support for for integrative analysis of microbiome and metabolomics feature lists (02/06/2023);
  • Added support for both 2012 version and 2013 version of Greengene database for PiCRUST (01/26/2023);
  • Updated KEGG global network for improved visualization and coverage (01/23/2023);
  • Added support for Sparse Estimation of Correlations among Microbiomes (SECOM) method in taxa correlation analysis (01/12/2023);
  • Minor bug fixes based on user feedback (12/27/2022);
  • Enhanced error messages when users upload normalized data instead of raw count table (12/22/2022);
  • Releasing MicrobiomeAnalyst 2.0 with three new modules coupled with many enhanced features in the existing modules (12/20/2022);
  • Expanded our taxon set libraries to include >5000 taxon sets covering 7 themes (12/18/2022);
  • Introducing a new module for ASV inference from 16S sequences based on DADA2 pipeline (12/16/2022);
  • Users can perform multi-factor association analysis based on MaAsLin2 (12/15/2022);
  • Interface enhancement and upgraded R to 4.2.2 (12/10/2022);
  • Fixed the issue for ASV file upload for Tax4Fun 2.0 (12/09/2022);
  • Added Metadata Editor (in Data Integrity Check page) to better support continuous metadata and covariate adjustment (12/05/2022);
  • Added support for interactive stacked bar/area plot - you can now zoom and mouse-over to get details (11/25/2022);
  • Added support for Tax4Fun 2.0 for prediction of functional profiles based on 16S rRNA data (11/15/2022);
  • Added support for Microbiome Regression-based Kernel Association Test (MiRKAT) in beta diversity analysis (11/14/2022);
  • Fixed Tax4Fun name mapping issue due to special characters (11/10/2022);
  • Added support for interactive heatmaps (11/08/2022);
  • Upgraded to PrimeFaces 12.0.0 (10/15/2022);
  • Added support for downloading sample / library size as a csv table (09/28/2022);
  • Enhanced message for metadata filtering (08/29/2022);
  • Fixed the taxonomy name issue when the input containing empty columns (07/29/2022);
  • Fixed the issue with heattree plot (07/13/2022);
  • Fixed the issue with parsing the "kingdom" column in the taxonomy table (06/29/2022);
  • Fixed the issue with PERMANOVA based on adonis2 (05/28/2022);
  • Interface enhancement and upgraded R to 4.1.3 (05/13/2022);
  • Added the support to adjust font size for heatmap visualization (03/02/2022);
  • Fixed the issue Heat tree and correction network issue introduced after R package updates (02/09/2022);
  • Fixed the issue with reading abundance table containing empty columns (01/28/2022);
  • Upgraded to PrimeFaces 11 (12/20/2021);
  • Fixed the issue in group-level stacked barplot in Abundance Profiling (10/18/2021);
  • Added support to switch the direction of comparison in heat tree analysis (08/31/2021);
  • Fixed some minor issues based on user comments (06/01/2021);
  • Bug fix for box plot at log scale (05/20/2021);
  • The web framework has been upgraded to PrimeFaces 10.0 (05/07/2021);
  • Fixed the issue with mouse clicking on node in SparCC correlation network (02/16/2021);
  • Bug fixing color palettes in Stacked Bar/Area Plots (01/11/2021);
  • Updated the KEGG global map (01/08/2021);
  • Added error handling for filtering step (01/06/2021);
  • Enhanced error message for handling user input (11/16/2020);
  • Fixed several issues associated with the new R version (09/24/2020);
  • Updated R from 3.6.2 to 4.0.2 (09/15/2020);
  • Updated Java to version 11 and Primefaces to 8.0 (04/08/2020)
  • Detailed guidance on MicrobiomeAnalyst is now available on Nature Protocols;
  • Enhanced correlation network visualization to display abundance piechart (02/12/2020);
  • Updated graph summary for correlation network, and added SparCC correlation in Pattern Hunter (02/03/2020);
  • Code refactoring for better performance (01/08/2020);
  • Added support for prepending higher taxonomic levels for stacked bar/area plots (12/06/2019);
  • Fixed meta-data update issue after editing data (11/21/2019);
  • Added support for zip file upload (11/18/2019);
  • Stacked area plot now supports grouping (faceting) based on two factors (10/24/2019);
  • Updated R from 3.5.1 to the latest version (3.6.1) (10/16/2019);
  • Fixed the issue with core microbiome analysis (09/18/2019);
  • Added support for group-wise core microbiome analysis (08/30/2019);
  • Added support for group-wise and sample-wise heat tree analysis (08/28/2019);
  • Minor bug fixes based on user feedback (08/26/2019);
  • Added support for SparCC correlation network analysis (08/15/2019);
  • Code refactoring and performance enhancements (08/01/2019);
  • ASV sequences are now mapped to self-defined ASV IDs for easy display and plotting (07/20/2019);
  • Added support for the viridis color palettes (07/10/2019);
  • Added support to label only significant nodes in heat tree graph (07/09/2019);
  • Code refactoring for improved performance(06/21/2019);
  • Updated the tutorial for marker gene profiling (MDP) module (06/15/2019);
  • Added support for heat tree visualization based on the Metacoder package (06/13/2019);
  • Added the R command history panel together with release of the companion R package MicrobiomeAnalystR (05/29/2019);
  • Upgraded the web framework to Primefaces 7.0 (05/19/2019);
  • Fixed the issue with data uploading issue in PPD module; (05/06/2019);
  • Minor feature enhancements (data processing and beta-diversity calculation) based on user feedback (MDP); (04/09/2019);
  • Added a "None" option to allow viewing abundance profile for all samples (MDP) (03/25/2019);
  • The rarefaction curve analysis now offers Good'd coverage table for download (MDP) (03/08/2019);
  • Added more data integrity check to ensure the same sample names between meta-data and OTU table (03/01/2019);
  • Added support for different facet views for abundance profiling (MDP) (02/15/2019);
  • Added support for rarefaction curve analysis (MDP) (02/01/2019);
  • Added support for tree file upload and phylogenetic tree analysis (01/015/2019);
  • Minor bug fixes and performance optimization (01/04/2019);
  • Expanded taxon set knowledgebase - now containing 2393 taxon sets organized into 11 libraries (12/08/2018);
  • Improved the the abundance profiling plot for better visualization (11/15/2018);
  • Text updates and minor interface improvement (09/19/2018);
  • Added F-values for PERMANOVA output (08/03/2018);
  • Features now require to appear in at least two samples instead of one to be retained (05/21/2018);
  • Diversity estimations are now based on filtered (and rarefied) data, instead only on raw counts (05/18/2018);
  • Added more error checking functions and code refactoring to reduce memory footprint (05/14/2018);
  • Fixed the issue with Tax4Fun results (now all integer counts) (05/10/2018);
  • Fixed the issue for TSEA network display (05/09/2018);
  • Fixed the issue for missing group information (05/07/2018);
  • Code cleaning and refactoring for performance gain (05/03/2018);
  • Added support for PICRUSt created biom file for SDP module (04/03/2018);
  • Minor bug fix for data normalization and core microbiome calculation (03/29/2018);
  • Minor bug fixes for metadata handling and support (03/6/2018);
  • Enhanced PDF generation feature and minor bug fixed (02/16/2018);
  • Updated code to reduce memory issue for PICRUSt computing (01/28/2018);
  • Added support to deal with continuous meta-data variables (01/22/2018);
  • Updated Phyloseq (R package) to deal with the weighted UniFrac distance issue during beta-diversity analysis (01/20/2018);
  • Added function for PDF report generation for each module (01/16/2018);
  • Minor bug fixes for taxonomy mapping and code refactoring (01/08/2018);
  • Enhanced support to deal with complex meta-data (12/21/2017);
  • Updated PDF tutorials based on recent changes (12/07/2017);
  • Added 1520 higher-level taxon sets associated with host (human) genetic variations (11/17/2017);
  • Enhanced error handling during parsing user input data (11/13/2017);
  • Added support for filtering minor taxa in piechart visualization (11/10/2017);
  • Bug fix for LEfSe table generation (11/07/2017);
  • Added a new PDF tutorial for MicrobiomeAnalyst overview (10/27/2017);
  • Bug fix for taxa labels changes after rarefying (10/24/2017);
  • Bug fix for sample editor (10/05/2017);
  • Minor bug fix for taxonomy file parsing issue (09/18/2017);
  • Code refactoring for performance improvement (09/15/2017);
  • Interface improvement and minor bug fixes (09/03/2017);
  • Fixed the color consistency issue with interactive piechart (09/01/2017);
  • Added support to merge small taxa for abundance profiling based on either sum or median abundance (08/31/2017);
  • Improved color schemes for barplot and piechart in abundance profiling (08/30/2017);
  • Fixed bugs and enhanced support for parsing mothur output (08/15/2017);
  • Added support for correlation analysis (07/25/2017);
  • Core microbiome analysis is now added (06/20/2017);
  • Added support to download result table from alpha and beta diversity analyses (06/09/2017);
  • Added 5 public datasets from environmental metagenomics studies for PPD; (06/07/2017);
  • Updated support for mothur output (05/11/2017);
  • Fixed the bug for boxplot image display (05/03/2017);
  • Improved code for faster taxonomic binning (04/28/2017);
  • Added support for generating PDF and SVG images for all major graph outputs (04/03/2017);
  • Bug fixes for CSS normalization on OTU data (03/22/2017);
  • Metabolic network now shows the matched KO members for current pathway (03/20/2017);
  • Updated FAQs based on user feedback (03/08/2017);
  • Added 38 species sets (now 174 in total) collected from over 25 publications (03/03/2017);
  • Improved barplot and piechart visualization based on user requests (03/01/2017);
  • Updated tutorials to support both Video and PDF versions (02/24/2017);
  • Users can now double click an edge in metabolic network to view reaction details (02/14/2017);
  • Added support for interactive enrichment network for TSEA (02/10/2017);
  • Added support for history view in PPD (01/25/2017);
  • Added 108 species-level taxon sets and 40 higher level taxon sets (01/15/2017);
  • Added support for rarefaction curve analysis (01/05/2017);
  • Enhanced point-and-click support for PCoA 3D visualization (01/04/2017);
  • Added support for normalization based on rarefying for minimum library size (12/28/2016);
  • Added support for parametric and non-parametric t-test/ANOVA (12/20/2016);
  • Added support for projecting user data with public 16S rRNA studies (12/10/2016);
  • Added support for Taxon Set Enrichment Analysis(11/15/2016);
  • Added support for network association analysis (SPEC-EASI) (10/15/2016);
  • Added metagenomeSeq for differential analysis (09/30/2016);
  • Added support for LEfSE (Linear discriminant analysis effect size) (09/20/2016);
  • Added support for shotgun metagenomic data analysis (09/10/2016);
  • Added support for Tax4Fun for prediction of metabolic potential (08/26/2016);
  • Added support for PiCRUST for prediction of metabolic potential (08/15/2016);
  • Added support for BIOM format and MOTHUR output files (07/08/2016);
  • MicrobiomeAnalyst test release (06/15/2016);