scanpy-scrna-seq
CommunityAnalyze single-cell RNA-seq data
Education & Research#bioinformatics#single-cell#dimensionality reduction#clustering#scanpy#gene expression#scrna-seq
Authorjaechang-hits
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill automates the complex process of analyzing single-cell RNA-seq data, from raw counts to annotated cell types, enabling rapid biological insights.
Core Features & Use Cases
- End-to-End Workflow: Handles QC, normalization, dimensionality reduction (PCA, UMAP), clustering (Leiden), and marker gene identification.
- Publication-Ready Output: Generates annotated datasets and visualizations suitable for scientific publications.
- Use Case: Analyze a new single-cell dataset to identify distinct cell populations, their marker genes, and potential cell states, producing figures for a research paper.
Quick Start
Load your 10X Genomics data, perform quality control, normalize, identify highly variable genes, run PCA and UMAP, cluster cells using Leiden, and identify marker genes.
Dependency Matrix
Required Modules
scanpyleidenalgigraphanndata
Components
scriptsreferences
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: scanpy-scrna-seq Download link: https://github.com/jaechang-hits/SciAgent-Skills/archive/main.zip#scanpy-scrna-seq Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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