scanpy skill

Scanpy: Single-Cell Analysis

Overview

Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis. Current stable release: scanpy 1.12.x (January 2026).

Installation

Requires Python 3.12+ (scanpy 1.12 dropped Python ≤3.11) and anndata ≥0.10.

uv pip install "scanpy[leiden]"

The [leiden] extra installs python-igraph and leidenalg, required for Leiden clustering. For reproducible environments, pin a version: uv pip install "scanpy[leiden]==1.12.1".

For large or out-of-core datasets, many functions support Dask arrays (experimental):

uv pip install "scanpy[leiden]" dask

See the Using dask with Scanpy tutorial. For GPU-accelerated scanpy-like operations, use rapids-singlecell as a separate package.

If the input is an R-native single-cell object (.rds, .RData, Seurat, or SingleCellExperiment), first convert it to .h5ad with R tooling, then load it with Scanpy. Read references/r_interop.md for agent-run installation and conversion instructions across macOS, Linux, and Windows.

For AnnData structure and I/O details, use the anndata skill. For probabilistic models and batch correction, use scvi-tools.

When to Use This Skill

This skill should be used when:

• Analyzing single-cell RNA-seq data (.h5ad, 10X, CSV formats)
• Working with R-friendly single-cell datasets (.rds, .RData, Seurat, SingleCellExperiment) that need conversion to .h5ad
• Performing quality control on scRNA-seq datasets
• Creating UMAP, t-SNE, or PCA visualizations
• Identifying cell clusters and finding marker genes
• Annotating cell types based on gene expression
• Conducting trajectory inference or pseudotime analysis
• Generating publication-quality single-cell plots

Script Toolkit (prefer these over writing code from scratch)

This skill bundles ready-to-run CLI scripts in scripts/ for every common step. Run these instead of hand-writing scanpy code — they handle file loading by extension, figure setup, sensible defaults, raw-count preservation, and progress logging. Each reads and writes .h5ad, so they chain together, and each has its own --help. Only drop down to writing scanpy code when a task isn't covered by a script or needs unusual customization.

All scripts use a shared scripts/_common.py helper (loading, saving, figure config) — keep it alongside the others. Run from the skill directory or pass full paths; figures default to ./figures/.

One-shot end-to-end run

# Counts → clustered, marker-annotated object + figures + marker CSVs
python scripts/run_pipeline.py raw.h5ad -o processed.h5ad \
    --resolution 0.5 --n-top-genes 2000 --scrublet
# With multi-sample integration:
python scripts/run_pipeline.py raw.h5ad -o processed.h5ad --batch-key sample --batch-method harmony
# Reproducible parameters via JSON (keys mirror flag names with underscores):
python scripts/run_pipeline.py raw.h5ad -o processed.h5ad --config params.json

Step-by-step chain (when you need to inspect/iterate between stages)

python scripts/qc_analysis.py        raw.h5ad  -o qc.h5ad   --scrublet
python scripts/preprocess.py         qc.h5ad   -o norm.h5ad --n-top-genes 2000
python scripts/reduce_dimensions.py  norm.h5ad -o red.h5ad  --n-pcs 40
python scripts/cluster.py            red.h5ad  -o clu.h5ad  --resolution 0.3 0.5 0.8
python scripts/find_markers.py       clu.h5ad  -o clu.h5ad  --groupby leiden --use-raw
# inspect results/markers/*.csv, decide labels, write a mapping JSON, then:
python scripts/annotate.py           clu.h5ad  -o ann.h5ad  --mapping celltypes.json

The sections below document the underlying scanpy calls each script performs — read them when customizing beyond the script flags.

Quick Start

Basic Import and Setup

import scanpy as sc
import pandas as pd
import numpy as np

# Configure settings
sc.settings.verbosity = 3
sc.settings.set_figure_params(dpi=80, facecolor='white')
sc.settings.figdir = './figures/'
sc.settings.autosave = True  # Preferred over per-plot save= (deprecated in scanpy 1.12)

Loading Data

# From 10X Genomics
adata = sc.read_10x_mtx('path/to/data/')
adata = sc.read_10x_h5('path/to/data.h5')

# From h5ad (AnnData format)
adata = sc.read_h5ad('path/to/data.h5ad')

# From CSV
adata = sc.read_csv('path/to/data.csv')

For R-native files, do not try to parse Seurat .rds directly in Python. Convert first:

# See references/r_interop.md for installing R and conversion packages.
Rscript convert_rds_to_h5ad.R input.rds output.h5ad

adata = sc.read_h5ad('output.h5ad')

Understanding AnnData Structure

The AnnData object is the core data structure in scanpy:

adata.X          # Expression matrix (cells × genes)
adata.obs        # Cell metadata (DataFrame)
adata.var        # Gene metadata (DataFrame)
adata.uns        # Unstructured annotations (dict)
adata.obsm       # Multi-dimensional cell data (PCA, UMAP)
adata.raw        # Raw data backup

# Access cell and gene names
adata.obs_names  # Cell barcodes
adata.var_names  # Gene names

Standard Analysis Workflow

The seven steps, with code and the parameters that matter at each, are in references/analysis_workflow.md:

before choosing thresholds rather than copying defaults.

1. Quality control — filter cells and genes; inspect mitochondrial fraction and counts

genes, and keep .raw for later plotting.

1. Normalization and preprocessing — normalize, log-transform, select highly variable

1. Dimensionality reduction — PCA, then the neighbour graph, then UMAP.
2. Clustering — Leiden at a resolution chosen for the question, not the default.
3. Marker gene identification — ranked genes per cluster.
4. Cell type annotation — mapping clusters to types from markers.
5. Save results — writing the annotated AnnData.

Common follow-on tasks — publication plots, trajectory inference, pseudobulk differential expression between conditions, gene set scoring, and batch correction — are in the same file. See also references/standardworkflow.md and references/plottingguide.md.

Key Parameters to Adjust

Quality Control

• min_genes: Minimum genes per cell (typically 200-500)
• min_cells: Minimum cells per gene (typically 3-10)
• pctcountsmt: Mitochondrial threshold (typically 5-20%)

Normalization

• target_sum: Target counts per cell (default 1e4)

Feature Selection

• ntopgenes: Number of HVGs (typically 2000-3000)
• minmean, maxmean, min_disp: HVG selection parameters

Dimensionality Reduction

• n_pcs: Number of principal components (check variance ratio plot)
• n_neighbors: Number of neighbors (typically 10-30)

Clustering

• resolution: Clustering granularity (0.4-1.2, higher = more clusters)

Common Pitfalls and Best Practices

1. Always save raw counts: adata.raw = adata before filtering genes
2. Check QC plots carefully: Adjust thresholds based on dataset quality
3. Use Leiden clustering: sc.tl.louvain is deprecated in scanpy 1.12
4. Try multiple clustering resolutions: Find optimal granularity
5. Validate cell type annotations: Use multiple marker genes
6. Use useraw=True for gene expression plots**: Shows normalized counts from .raw
7. Check PCA variance ratio: Determine optimal number of PCs
8. Save intermediate results: Long workflows can fail partway through
9. Pseudobulk for DE: Do not treat rankgenesgroups p-values as rigorous DE between conditions
10. Save plots via settings: Use sc.settings.autosave instead of deprecated save= on plot functions
11. Convert R objects before Scanpy: Use R packages to convert Seurat or SingleCellExperiment .rds files to .h5ad, preserving counts, metadata, and gene identifiers

Bundled Resources

scripts/ (CLI toolkit)

A composable set of .h5ad-in/.h5ad-out scripts covering the whole workflow plus a one-command end-to-end pipeline. See the Script Toolkit section above for the full table and chaining examples. Each script has --help. Files:

• _common.py — shared loading/saving/figure helpers imported by the others (not a CLI)
• run_pipeline.py — full pipeline in one command (flags or --config JSON)
• inspect_data.py, convert.py — explore and load/convert any input format
• qcanalysis.py, preprocess.py, reducedimensions.py, batch_correct.py, cluster.py — pipeline steps
• findmarkers.py, annotate.py, scoregenes.py, pseudobulk.py — markers, annotation, scoring, DE prep
• subset.py, plot.py — subset by metadata/genes; generate any standard plot

Default to these scripts before writing scanpy code from scratch.