single-cell-basic-analysis
CommunityEnd-to-end scRNA-seq analysis with NumPy.
AuthorMDhewei
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Automates end-to-end single-cell RNA-seq analysis from raw count matrices, including QC filtering, normalization, HVG selection, dimensionality reduction (PCA + UMAP), clustering, and marker gene discovery, using a pure NumPy/Pandas workflow for educational and exploratory use.
Core Features & Use Cases
- End-to-end preprocessing: QC filtering, normalization, HVG selection, PCA, and clustering.
- Marker discovery: Wilcoxon-based tests with BH-FDR correction to identify cluster markers.
- Educational/educational-leaning: avoids heavy dependencies while producing publication-ready outputs for small to medium datasets.
Quick Start
Run the pipeline on a counts matrix by invoking the Python script with your input file and an output directory.
Dependency Matrix
Required Modules
pandasnumpymatplotlibscipy
Components
scripts
💻 Claude Code Installation
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Please help me install this Skill: Name: single-cell-basic-analysis Download link: https://github.com/MDhewei/bioinfor-claw/archive/main.zip#single-cell-basic-analysis Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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