Before You Start

Downstream analyses assume you already completed Upload, Preprocess, and Embedding. Use Check Readiness to validate UUID/session and embedding availability.

Trajectory (PAGA + DPT)

Produces pseudotime estimates. The most critical parameter is the root definition. If biological prior exists (early progenitor cluster), use root_strategy=cluster.

• Output: pseudotime CSV + UMAP pseudotime plot.
• Risk: wrong root leads to biologically inverted trajectories.

RNA Velocity (scVelo)

Requires spliced/unspliced layers. Default mode stochastic is robust for many datasets. Use dynamical only when data quality and depth justify model complexity.

• Output: velocity stream plot (PNG, native scVelo) + interactive stream-like overlay (Plotly HTML) + interactive velocity score plot (HTML) + per-cell velocity score CSV.
• Failure mode: missing layers or low kinetic signal.

SCENIC (pySCENIC)

Executes full CLI pipeline: grn -> ctx -> aucell. Requires configured resources in backend env vars (PYSCENIC_*).

• Output: adjacencies, regulons, AUCell matrix, regulon activity UMAP.
• Default: minimum regulon gene count = 20.

SCENIC Advanced Analysis

This post-processing block appears only after SCENIC completes. It reuses existing SCENIC outputs and adds regulon-level summaries, binarization QC, RSS-based specificity views, optional t-SNE in regulon space, and TF-target network views.

• Output: AUCell/group heatmaps, binary activity heatmap, RSS heatmap + top RSS bars, optional t-SNE, and regulon network.
• Cost: much lighter than full SCENIC; no GRN/CTX rerun.

CellChat (Python via LIANA)

Runs LIANA's CellChat method to score ligand-receptor communication between groups. Group sizes strongly affect stability; keep min_cells_per_group realistic.

• Output: interaction table, source-target edges, CellChat probability heatmap, CellChat circle network, CellChat bubble plot, LIANA dotplot, and LIANA sender/receiver heatmap.
• Default: min_cells_per_group=10, database auto by species.