MicrobiomeAnalyst

-- comprehensive statistical, visual and meta-analysis of microbiome data

Starting from marker gene abundance data (OTU table, BIOM file, mothur output)

Visually exploring your 16S rRNA data with a public data in a 3D PCoA plot

Starting from gene list or gene abundance data annotated by KO, EC or COG

Starting with a list of taxa of interest (strains, species or higher level taxa)

MDP

Marker Data Profiling (MDP): Comprehensive composition & diversity analysis supporting various methods of data overview, alpha diversity and beta-diversity; comparative analysis supporting multiple differential abundance methods (metagenomeSeq, LEfSe, edgeR, DESeq2, etc.); as well as prediction of metabolic potentials.

SDP

Shotgun Data Profiling (SDP): Functional diversity profiling based on KEGG annotations (modules, pathways, metabolisms, EC) or COG categories, direct functional association testing, as well as differential abundance analysis followed by functional enrichment analysis within a powerful metabolic network visualization system.

TSEA

Taxon Set Enrichment Analysis (TSEA): Enrichment analysis using ~2400 manually collected taxon sets organized into 11 different categories. They are defined based on their shared phenotypic traits or ecological niches, or their associations with host genetic variations, lifestyles, biochemistry, diseases, developmental stages, etc.

PPD

Projection with Public Data (PPD): Co-processing your data together with a suitable public 16S rRNA data of interest and explore the results within an interactive 3D PCoA visualization system to easily discover patterns of interest as well as to associate these patterns with the underlying taxonomic variations.

News & Updates

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 (03/06/2018);
Minor bug fix for parsing user input (03/01/2018);
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 136 species-level taxa sets and 40 higher level taxa sets (01/15/2017);
Added support for rarefaction curve analysis (01/05/2017);

Read more ......

Please cite:

Dhariwal, A., Chong, J., Habib, S., King, I., Agellon, LB., and Xia. J. (2017) "MicrobiomeAnalyst - a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data"
Nucleic Acids Research 45 W180-188 (doi: 10.1093/nar/gkx295)