skills.rest
Yezez9
Yezez9COMMUNITY
Explore all skills by this author →
GitHub

scanpy

Analyze single-cell RNA-seq data with quality control, clustering, and differential expression.

Updated Mar 10, 2026
Search Tags:#data analysis#bioinformatics#genomics#single-cell#scanpy#scrna-seq
One-click install
npx skills add https://github.com/Yezez9/Research-Agent --skill scanpy-yezez9
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: scanpy
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/scanpy
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill scanpy-yezez9

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

This Skill streamlines the complex process of analyzing single-cell RNA-seq data, enabling researchers to quickly gain insights into cellular heterogeneity and function.

Core Features & Use Cases

  • End-to-End Analysis: Handles the entire scRNA-seq workflow from QC to visualization.
  • Standardized Workflows: Implements best practices for normalization, dimensionality reduction, clustering, and marker gene identification.
  • Use Case: A biologist has generated scRNA-seq data and needs to identify distinct cell populations, find marker genes for each population, and visualize the results. This Skill can perform all these steps automatically.

Quick Start

Use the scanpy skill to perform a standard single-cell RNA-seq analysis on the provided 'expression_matrix.h5ad' file.

Frequently Asked Questions about scanpy

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I analyze single-cell RNA-seq data from an h5ad file?▼

Yes, single-cell RNA-seq analysis integrates natively with AnnData objects, allowing you to handle expression matrices and visualize cellular heterogeneity directly within the established bioinformatics pipeline without manual format conversion.

Can I use AnnData objects for single-cell RNA-seq quality control and normalization?▼

Yes, single-cell RNA-seq analysis integrates natively with AnnData objects, allowing you to handle expression matrices and visualize cellular heterogeneity directly within the established bioinformatics pipeline without manual format conversion.

What is the standard workflow for identifying cell types in scRNA-seq data?▼

No external dependencies are required to run the single-cell RNA-seq analysis pipeline, but you need a valid AnnData h5ad expression matrix as input to automatically execute the end-to-end bioinformatics workflow and generate visualizations.

Do I need any external dependencies to run scRNA-seq clustering and visualization?▼

No external dependencies are required to run the single-cell RNA-seq analysis pipeline, but you need a valid AnnData h5ad expression matrix as input to automatically execute the end-to-end bioinformatics workflow and generate visualizations.

What's the best way to find marker genes for distinct cell populations in genomics data?▼

Single-cell RNA-seq analysis covers the entire workflow from raw expression matrices through quality control, normalization, dimensionality reduction, clustering, and differential expression, outputting visualizations of cellular heterogeneity and identified cell types.

Related Skills

Explore More Education & Research Skills→
zongtingweizongtingwei
25

scrna-preprocessing-clustering

Preprocess single-cell RNA-seq data into analysis-ready AnnData objects.

Community
Advanced
anthropicsanthropics
568

single-cell-rna-qc

Filter low-quality cells from single-cell RNA-seq data using MAD-based QC.

Official
Intermediate
cas-bigdatalabcas-bigdatalab
541

bdbe_scnorm

Normalize single-cell sequencing expression matrices from h5ad and CSV files.

Official
Advanced
frumu-aifrumu-ai
114

bio-single-cell

Perform deep learning-based single-cell RNA sequencing analysis with scvi-tools.

Official
Intermediate