spatial-de
OfficialDiscover single-cell marker genes.
AuthorTianGzlab
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill automates the identification of marker genes in single-cell RNA sequencing data, which is crucial for understanding cell populations and biological states, preventing users from manually configuring complex statistical tests with inconsistent parameters.
Core Features & Use Cases
- Marker Gene Discovery: Identifies genes that define cell clusters or differentiate between experimental conditions using robust statistical methods (Wilcoxon, t-test, MAST, DESeq2 pseudo-bulk).
- Automated Visualization: Generates essential plots like Volcano plots, MA plots, and dotplots for clear interpretation of results.
- Use Case: Analyze a single-cell dataset to find the top 10 genes that distinguish 'Tumor' cells from 'Normal' cells, and visualize these markers with a dotplot.
Quick Start
Use the sc-de skill to find marker genes for all clusters in the file 'annotated.h5ad'.
Dependency Matrix
Required Modules
scanpypandasmatplotlibdecouplerpydeseq2rpy2
Components
scriptsreferencesassets
💻 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: spatial-de Download link: https://github.com/TianGzlab/OmicsClaw/archive/main.zip#spatial-de Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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