| AnnData | Annotated data matrix format (.h5ad) used internally for all modalities |
| Checkpoint | Intermediate processed .h5ad written between pipeline steps |
| Contrast | A saved comparison between two groups (for example treatment vs control) |
| DE | Differential expression — genes that change between groups or clusters |
| Domain | Spatial cluster of spots representing a tissue region |
| Enrichment | Statistical over-representation of genes in curated pathways (GO, KEGG) |
| Experiment | Database/API name for a study |
| HVG | Highly variable gene — selected before dimensionality reduction |
| Leiden | Graph-based clustering algorithm used after neighbor graph construction |
| Metadata | Sample or cell annotations merged into AnnData obs |
| Modality | Assay type: single-cell, bulk, or spatial |
| ORA | Over-representation analysis — enrichment method used in the current UI |
| Pipeline run | One execution of an analysis step with saved parameters and results |
| Provenance | Record of how a result was produced (parameters, versions, inputs) |
| Pseudobulk | Aggregating single-cell counts to sample level before DE (planned) |
| QC | Quality control — filtering low-quality cells or samples |
| Run | See pipeline run |
| Snapshot | Frozen study state referencing specific runs and parameters |
| Stale | Result outdated because upstream data or parameters changed |
| Study | Top-level project container in the UI |
| SVG | Spatially variable gene — expression varies across tissue coordinates |
| UMAP | 2D embedding for visualizing cell similarity |
| Wilcoxon | Non-parametric test used for rank-based DE in the current pipeline |