Table 1.
Comparison of MicrobiomeAnalyst2.0 with other web tools. Symbols used for feature evaluations with ‘-’ for absent and ‘+’ for a more quantitative assessment (more ‘+’ indicating better support, e.g. better visualization and more options provided). The URLs for each tool are given below
| Tools | MicrobiomeAnalyst | VAMPS | Namco | gcMeta | MIAN | |
|---|---|---|---|---|---|---|
| 2.0 | 1.0 | |||||
| Platform | Web | Web | Web (registration) | R Shiny | Web (registration) | Web (registration) |
| Input | FASTQ, count tables, BIOM, mothur | Same as 2.0 except FASTQ | FASTQ | FASTQ | FASTQ | Count tables; BIOM |
| Community profiling | ||||||
| Diversity | +++ | +++ | + | ++ | – | ++ |
| Clustering | +++ | ++ | – | ++ | – | – |
| Correlation | +++ | ++ | – | ++ | – | ++ |
| Statistical analysis | ||||||
| Processing | +++ | +++ | ++ | ++ | + | ++ |
| Comparison | Single/multi- factors | Single factor | Single factor | Single/multi-factor | Single factor | Single factor |
| Biomarker | ++ | ++ | – | ++ | + | +++ |
| Time series | + | – | – | ++ | – | – |
| Functional profiling | ||||||
| Functional prediction | PICRUSt, Tax4Fun, Tax4Fun2 | PICRUSt, Tax4Fun | – | PICRUSt2 | PICRUSt | – |
| Functional annotation | COG, KEGG, GEM | COG, KEGG | – | KEGG | KEGG | – |
| Network visualization | Contextualized | Generic | – | – | – | – |
| Co-analysis with metabolomics data | ||||||
| Dimension reduction | Procrustes & DIABLO | – | – | – | – | – |
| Pathway enrichment | KO, targeted or untargeted metabolomics | – | – | – | – | – |
| Correlation analysis | Statistical and GEM based correlation | – | – | – | – | – |
| Meta-analysis | ||||||
| Visual exploration | + | – | – | – | – | – |
| Statistical analysis | + | – | – | – | – | – |
| Integration with public data | + | + | + | – | – | – |
| Taxon set analysis | ++ | + | – | – | – | – |
VAMPS: https://vamps2.mbl.edu/; gcMeta: https://gcmeta.wdcm.org; Namco: https://exbio.wzw.tum.de/namco; MIAN: https://miandata.org/projects.