Scanpy inputs and parameters
Input format and every QC, feature-selection, clustering, and DE parameter for Scanpy.
You provide one AnnData .h5ad file plus the parameters for your chosen workflow. The values that most affect the result are the QC cutoffs — minimum genes per cell, maximum mitochondrial percent, and the number of highly variable genes — because they decide which cells and genes survive into clustering. Everything else has a sensible default keyed to the GPU pipeline.
Input format
The platform's Scanpy job reads a single AnnData .h5ad file from storage. The URL must be an S3 URI (s3://…) or an HTTPS URL (https://…) and must end in .h5ad — the pipeline validates both.
| Requirement | Detail |
|---|---|
| Format | AnnData (.h5ad) only |
| Location | S3 URI or HTTPS URL |
| Contents | Cells × genes count matrix in X, gene symbols in var |
If you have 10X Cell Ranger output, a CSV count matrix, or another format, convert it to .h5ad before submitting.
Workflow selection
| Value | What runs |
|---|---|
full (default) | QC → normalize → HVG → PCA → UMAP → Leiden → differential expression |
qc | Quality control and filtering only |
clustering | QC through Leiden clustering + UMAP (no markers) |
de | Differential expression / marker genes |
The tool also exposes CPU-based extension workflows — harmony_integrate, scanorama_integrate, combat_correct (batch correction), celltypist_annotate (annotation), aucell_score, cosg_markers, hotspot_modules, cytotrace2_potency, scvelo_velocity. Batch-correction workflows require a batch_key naming the obs column with sample labels.
Quality-control parameters
| Parameter | Range | Default | What it does |
|---|---|---|---|
min_genes | 1–5000 | 200 | Drop cells with fewer detected genes (empty droplets) |
min_cells | 1–100 | 3 | Drop genes seen in fewer cells |
max_genes | integer | none | Optional upper bound (possible doublets) |
max_mito_percent | 0–50 | 5 | Drop cells above this mitochondrial fraction (dying cells) |
The platform defaults to a 5% mitochondrial cutoff — stricter than the 20% often seen in tutorials. Relax max_mito_percent if QC filters out too many cells (a common cause of an "empty after filtering" error).
Feature selection and dimensionality reduction
| Parameter | Range | Default | What it does |
|---|---|---|---|
n_top_genes | 100–10000 | 2000 | Number of highly variable genes to keep |
hvg_flavor | cell_ranger · seurat · seurat_v3 | seurat | HVG selection method |
n_pcs | 2–100 | 50 | Principal components for the neighbor graph |
n_neighbors | 2–100 | 15 | Neighbors in the kNN graph |
Clustering and differential expression
| Parameter | Range | Default | What it does |
|---|---|---|---|
resolution | 0.1–2.0 | 1.0 | Cluster granularity — higher gives more, smaller clusters |
clustering_method | leiden · louvain | leiden | Community-detection algorithm |
method | wilcoxon · t-test · logreg | wilcoxon | Marker-gene ranking test |
de_groups | list | none | Restrict DE to specific clusters |
Output options
| Parameter | Default | What it does |
|---|---|---|
generate_figures | true | Produce UMAP and violin plots |
figure_format | png | png, pdf, or svg |
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