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Scanpy

Maintainer K-Dense Inc. · Last updated April 1, 2026

Scanpy is a scalable Python toolkit for analy.

Claude CodeOpenClawNanoClawAnalysisWritingscanpybioinformaticspackagebioinformatics & genomics

Original source

K-Dense-AI/claude-scientific-skills

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/scanpy

Maintainer: K-Dense Inc.
License: SD-3-Clause license
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

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.
sc.settings.verbosity = 3 sc.settings.set_figure_params(dpi=80, facecolor='white') sc.settings.figdir = './figures/'.

Source Doc

Excerpt From SKILL.md

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')