metabolomics - nsalomonis/altanalyze GitHub Wiki

Metabolomics experiments typically produce quantitative values associated with chemical identifiers (PubChem, KEGGcompound, HMDB, ChEBI, CAS). AltAnalyze supports import and analysis of metabolomics data assuming:

• IDs correspond to one of the above chemical ID systems
• Quantitative values are non-zero (ideally log₂)

Input IDs do not have to correspond to one of the above, but will if annotations and enrichment analyses are desired in AltAnalyze. Supported analyses include:

1. Differential metabolite expression statistics (e.g., moderated t-test)
2. Metabolite annotation (e.g., name, KEGG, WikiPathways)
3. Sample classification (LineageProfiler)
4. Marker prediction (MarkerFinder)
5. Quantile and batch-effects normalization
6. Hierarchical clustering
7. 2D and 3D PCA
8. Basic sample QC visualization
9. Pathway enrichment analysis and visualization

To import data, simple select the Vendor/data-type as Other ID and the appropriate ID system under the menu Select platform. Proceed with the default or customized options.