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 a large collection of taxon sets including 105 strain-level taxon sets, 174 species-level taxon sets and 40 mixed level taxon sets, based on their shared phenotypic traits or ecological niches, or associations with host 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

  • 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)

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