forge¶
The wiki for GrAndMA — a web platform for multi-omics data analysis.
GrAndMA lets you upload metabolomics, transcriptomics, microbiome, proteomics, or other tabular omics datasets and run preprocessing, statistical analysis, clustering, biomarker discovery, and network analysis in a browser — no coding required.
forge is the canonical reference for using GrAndMA.
Start here¶
- Getting Started — upload your first dataset and run an analysis end-to-end
- Data Formats — accepted file formats and how to structure your data
- Demo Datasets — 14 built-in studies you can explore without uploading anything
Analyses¶
- Preprocessing — normalisation, imputation, log transformation, batch correction
- Statistical Analysis — differential abundance, correlation, longitudinal models
- Clustering — PCA, UMAP, hierarchical, k-means
- Network Analysis — metabolite networks and pathway enrichment
- Multi-Omics — JIVE, MOFA+, SNF, MCIA, DIABLO
- Biomarker Discovery — elastic net + SHAP, survival analysis
- Untargeted Metabolomics — mzML processing and spectral annotation
Microbiome¶
Portal that hosts every microbiome-specific module. Each module is independently runnable; pick the one that answers your question.
- Microbiome overview — portal concepts, module registry, module gating
- GeMMA — community metabolic model + punch + concordance + Steiner subgraph
- HUMAnN3 — MetaCyc pathway differential from shotgun reads
- MaAsLin2 — feature ↔ metadata linear-model associations (coming soon)
Backend¶
- GIZMO — the metabolite knowledge graph that powers network and annotation features