| AI interpretation | Grounded narrative summary (cluster annotation, DE, enrichment, or study/methods text) generated from structured run results; cannot cite values absent from the run payload |
| Ambient RNA | Cell-free RNA in the droplet suspension that contaminates every cell's counts; estimated and removed SoupX- or decontX-style |
| AnnData | Annotated data matrix format (.h5ad) used internally for all modalities |
| Checkpoint | Intermediate processed .h5ad written between pipeline steps |
| cLISI | Cell-type local inverse Simpson's index — effective number of cell types around each cell after integration; near 1 means cell types stay separate |
| Composition testing | Testing whether cell-type proportions differ between conditions across biological replicates (propeller-style) |
| Contrast | A saved comparison between two groups (for example treatment vs control) |
| Coverage DEG | Multi-class biomarker step ranking genes by recurrence across all pairwise class comparisons |
| DE | Differential expression — genes that change between groups or clusters |
| Deconvolution | Estimating cell-type composition fractions from sample- or spot-level expression profiles |
| Disease evidence | Curated gene-disease association lookup applied to run-derived gene sets; research context, not diagnostic evidence |
| Domain | Spatial cluster of spots representing a tissue region |
| Doublet | A droplet that captured two cells; scored per sample (Scrublet-style or classifier) and optionally removed in QC |
| Enrichment | Statistical over-representation or ranking of genes against curated pathways (GO biological process and Reactome for human, mouse, and rat; a curated human KEGG subset) |
| Experiment | Database/API name for a study |
| GSEA | Gene set enrichment analysis — ranked whole-DE-table enrichment method, reported alongside ORA |
| HVG | Highly variable gene — selected before dimensionality reduction |
| iLISI | Integration local inverse Simpson's index — effective number of batches around each cell; higher means better mixed |
| Integration | Batch-correction step (Harmony or fastMNN) that removes sample/batch-driven structure from a joint PCA before clustering |
| 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, spatial, or biomarker |
| Niche | Lightweight spatial candidate region nominated from co-localizing, enriched tissue domains |
| ORA | Over-representation analysis — enrichment method for thresholded gene lists |
| Pipeline run | One execution of an analysis step with saved parameters and results |
| Preparation method comparison | Benchmark of sample-preparation protocols (enzymatic, fixed cells, nuclei) on recovery, quality, composition, and marker preservation |
| Provenance | Record of how a result was produced (parameters, versions, inputs) |
| Pseudobulk | Aggregating single-cell counts by sample and cell type/cluster, then running replicate-aware DE |
| Pseudotime | Graph-based ordering of cells along an inferred trajectory |
| QC | Quality control — filtering low-quality cells or samples |
| RNA velocity | Direction of change in each cell's expression, estimated from spliced vs unspliced counts |
| Run | See pipeline run |
| Single-cell CNV | Chromosome-scale copy-number inference from single-cell expression, used for malignant-cell and subclone calls |
| Sketch | Representative-cell downsampling and projection strategy for working with large single-cell datasets |
| Snapshot | Frozen study state referencing specific runs and parameters |
| Spliced fraction | Share of a cell's reads that are spliced; lower in nuclei (intron-rich) than in whole cells |
| ssGSEA | Single-sample gene set enrichment — per-sample or per-cell gene-set scores |
| Stale | Result outdated because upstream data or parameters changed |
| Stress signatures | Per-cell scores for heat shock, apoptosis, necrosis, senescence, UPR, oxidative stress, DNA damage, and immediate-early dissociation genes |
| Study | Top-level project container in the UI |
| SVG | Spatially variable gene — expression varies across tissue coordinates |
| Trajectory | Ordering of cell states (pseudotime) plus cell-cycle scoring for differentiation/activation analysis |
| UMAP | 2D embedding for visualizing cell similarity |
| WGCNA | Weighted gene co-expression network analysis — modules, hub genes, and eigengene-trait correlations |
| Wilcoxon | Non-parametric test used for rank-based DE in the current pipeline |