scanpy

Included with Lifetime

$97 forever

Scalable toolkit for analyzing single-cell gene expression data. Built on top of Anndata, focusing on clustering, trajectory inference, and visualization.

General

What this skill does


# Scanpy - Single-Cell Analysis

Scanpy processes high-dimensional biological data, reducing it via PCA/UMAP to identify rare cell populations in tissues or microbiomes.

## When to Use

- Analyzing single-cell RNA sequencing (scRNA-seq) data.
- Identifying cell types and states in heterogeneous tissues.
- Reconstructing developmental trajectories.
- Comparing cell populations between conditions.
- Discovering rare cell types.

## Core Principles

### AnnData Format

Scanpy uses AnnData objects that store expression matrix, cell metadata, and gene annotations together.

### Dimensionality Reduction

High-dimensional gene expression (20,000+ genes) is reduced to 2D/3D for visualization (PCA → UMAP/t-SNE).

### Clustering

Cells are grouped by similarity in gene expression space to identify cell types.

## Quick Reference

### Standard Imports

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

### Basic Patterns

```python
# 1. Load dataset (AnnData object)
adata = sc.read_h5ad("cells.h5ad")
# Or: adata = sc.read_10x_mtx("path/to/mtx")

# 2. QC and Normalization
sc.pp.filter_cells(adata, min_genes=200)
sc.pp.filter_genes(adata, min_cells=3)
sc.pp.normalize_total(adata, target_sum=1e4)
sc.pp.log1p(adata)

# 3. Dimensionality Reduction & Visualization
sc.pp.highly_variable_genes(adata)
sc.tl.pca(adata)
sc.tl.umap(adata)
sc.pl.umap(adata, color=['cell_type', 'gene_A'])

# 4. Clustering
sc.tl.leiden(adata, resolution=0.5)
sc.pl.umap(adata, color='leiden')
```

## Critical Rules

### ✅ DO

- **Set scanpy settings** - Use `sc.settings.verbosity = 3` for progress info.
- **Filter low-quality cells** - Remove cells with too few genes or high mitochondrial content.
- **Normalize before analysis** - Account for sequencing depth differences.
- **Use highly variable genes** - Focus analysis on informative genes.

### ❌ DON'T

- **Don't skip QC** - Low-quality cells can dominate clustering.
- **Don't use raw counts for PCA** - Always normalize and log-transform first.
- **Don't ignore batch effects** - Use batch correction (e.g., `sc.pp.harmony_integrate`) when combining datasets.

## Advanced Patterns

### Trajectory Inference

```python
import cellrank as cr

# Reconstruct developmental trajectories
sc.tl.paga(adata)
sc.pl.paga(adata)
adata.uns['iroot'] = np.flatnonzero(adata.obs['cell_type'] == 'stem')[0]
sc.tl.dpt(adata)
```

### Differential Expression

```python
# Find marker genes for each cluster
sc.tl.rank_genes_groups(adata, 'leiden', method='wilcoxon')
sc.pl.rank_genes_groups(adata, n_genes=20)
```

Scanpy has revolutionized single-cell biology, enabling researchers to map the cellular diversity of tissues and understand how cells differentiate and function.

Files: 1

Size: 2.9 KB

Complexity: 11/100

Category: General

Source: https://github.com/tondevrel/scientific-agent-skills/tree/main/skills/scanpy

Related in General

modeling-omnistudio-epc-catalog

Included

Salesforce Industries CME EPC product-modeling skill for Product2-based catalog creation. Use when creating EPC products, configuring product attributes, building offer bundles with Product Child Items, or reviewing EPC DataPack JSON metadata for product catalog changes. TRIGGER when: user creates or updates Product2 EPC records, AttributeAssignment payloads, AttributeMetadata/AttributeDefaultValues, Offer bundles, or ProductChildItem relationships. DO NOT TRIGGER when: designing OmniScripts/FlexCards/Integration Procedures (use building-omnistudio-omniscript, building-omnistudio-flexcard, or building-omnistudio-integration-procedure), implementing Apex business logic (use generating-apex), or troubleshooting deployment pipelines (use deploying-metadata).

Generalscripts

relationship-science-coach

Included

Use this skill for direct, practical adult relationship coaching: couples conflict, repair, trust, marriage, dating, flirting, attachment patterns, emotional connection, sex, desire differences, eroticism, kink negotiation, affection, love languages, breakups, and long-term passion. Draw on Gottman, EFT and Hold Me Tight, attachment science, modern sex research, Perel, Nagoski, Kerner, Schnarch, Love and Stosny, and flexible love-language tools. Be concrete and low-hedge. Redirect only for imminent danger, abuse, coercive control, minors, non-consent, self-harm, stalking, or medical/legal/psychiatric decisions.

Generalscripts

building-sf-integrations

Included

Salesforce integration architecture and runtime plumbing with 120-point scoring. Use this skill to set up Named Credentials, External Credentials, External Services, REST/SOAP callout patterns, Platform Events, and Change Data Capture. TRIGGER when: user sets up Named Credentials, External Services, REST/SOAP callouts, Platform Events, CDC, or touches .namedCredential-meta.xml files. DO NOT TRIGGER when: Connected App/OAuth config (use configuring-connected-apps), Apex-only logic (use generating-apex), or data import/export (use handling-sf-data).

Generalscripts

venue-templates

Included

Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and grant proposals (NSF, NIH, DOE, DARPA). This skill should be used when preparing manuscripts for journal submission, conference papers, research posters, or grant proposals and need venue-specific formatting requirements and templates.

Generalscripts

let-fate-decide

Included

Draws the 12 Houses of the Zodiac Tarot spread to inject entropy into planning when prompts are vague, ambiguous, or casually delegated. Interprets the spread to guide next steps. Use when the user says 'let fate decide', 'YOLO', 'whatever', 'idk', or other nonchalant phrases, makes Yu-Gi-Oh references, or when you are about to arbitrarily pick between multiple reasonable approaches. Prefer over ask-questions-if-underspecified when the user's tone is casual or playful rather than precision-seeking.

Generalscripts

net-ops

Included

Cross-platform network troubleshooting (Windows, macOS, Linux) via local or remote shell. Use for: DNS broken, can't resolve hostnames, nslookup/dig works but apps fail, NRPT, WFP, scutil, /etc/resolver, systemd-resolved, /etc/resolv.conf, NetworkManager, VPN DNS leak residue (ProtonVPN/Mullvad/WireGuard/AnyConnect), AV/firewall blocking DNS or DoH, Tailscale DNS interaction, intermittent connectivity, remote diagnostics over SSH.

Generalscripts