MicrobiomeAnalyst
-- comprehensive statistical, functional and integrative analysis of microbiome data
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Update History
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
);
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