Tutorials

The tutorials below use synthetic AnnData objects so no project data is required. They follow the pipeline phases described in API Reference.

1. Getting Started

End-to-end minimal workflow: load data, preprocess, score signatures, plot.

1. Getting Started

2. QC and Filtering

Phase 1 — QC metrics, spot filtering, cross-sample comparison, HTML report.

2. QC and Filtering

3. Preprocessing

Phase 3 — normalize, integrate (scVI / Harmony), cluster, UMAP.

3. Preprocessing

4. Gene Signature Scoring

Phase 3.5b — load Hallmark sets, score_signature, ORA, GSEA dot plot.

4. Gene Signature Scoring

5. Cell-type Deconvolution

Phase 3.5b — extract reference profiles, run deconvolution, inspect proportions.

5. Cell-type Deconvolution

6. Spatial Analysis

Phase 5 — colocalization, Morans I, neighborhood enrichment, spatial PDF.

6. Spatial Analysis