From: MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data
 | Feature | MetaboDirect | MetaboAnalyst | PyKrev | ftmsRanalysis | UME |
---|---|---|---|---|---|---|
Software appearance | User interface | Command line | Web GUI | Python module | R packagea | Web GUI |
Platform | Cross platform | |||||
Language | Python, R | R, Java | Python | R | R | |
Coding knowledge required | Minimalb | No | Yes | Yes | No | |
Open source | ✔ | |||||
Documentation | ✔ | |||||
Data pre-processing | Raw spectra processing | ✖ | ✔c | ✖ | ✖ | ✖ |
Mol. formula assignment | ✖ | ✔ | ✖ | ✖ | ✔ | |
Filtering and normalization | ✔ | |||||
Thermodynamic indices calculation | ✔ (DBE, GFE, AI, NOSC) | ✖ | ✔ (DBE, AI, NOSC) | ✔ (DBE, GFE, AI, NOSC) | ✔ (DBE) | |
Molecular class assignment | ✔ | ✖ | ✔ | ✔ | No | |
Data Exploration | Van Krevelen diagrams | ✔ | ✖ | ✔ | ✔ | ✔ |
Molecular composition plots | ✔ | ✖ | ✔ | ✖ | ✖ | |
Thermodynamic indices plots | ✔ | ✖ | ✔ | ✔ | ✔ | |
Chemodiversity indices | ✔ | ✖ | ✔ | ✖ | ✖ | |
Pairwise comparisons | ✔ | ✖ | ✖ | ✔ | ✖ | |
Database mapping | ✔ | ✔ | ✖ | ✔ | ✖ | |
Statistical analysis | PERMANOVA | ✔ | ✖ | ✖ | ✖ | ✖ |
NMDS | ✔ | ✖ | ✖ | ✖ | ✔ | |
PCA | ✔ | ✔ | ✔ | ✖ | ✖ | |
Molecular transformation network analysis | Transformation calculation | ✔ | ✖ | ✖ | ✖ | ✖ |
Network construction | ✔ | ✖d | ✖ | ✖ | ✖ | |
Network Analysis | ✔ | ✖d | ✖ | ✖ | ✖ | |
Extras | Customizable plots | ✔ | Limited | ✔ | ✔ | ✖ |
Multiple grouping variables | ✔ (up to 2) | ✖ | ✖ | ✔ | ✖ |