Scanpy

When to Use This Skill

This skill should be used when:

• Analyzing single-cell RNA-seq data (.h5ad, 10X, CSV formats)
• 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

Basic Import and Setup

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

## From 10X Genomics

adata = sc.read_10x_mtx('path/to/data/')
adata = sc.read_10x_h5('path/to/data.h5')