sc-preprocessing

What problem does it solve?

This Skill automates the complex and time-consuming initial steps of single-cell RNA sequencing data analysis, ensuring consistency and reproducibility.

Core Features & Use Cases

• Automated QC & Filtering: Applies standard quality control metrics to filter out low-quality cells and genes.
• Normalization & Scaling: Performs library size normalization and log transformation.
• Dimensionality Reduction & Clustering: Computes PCA, UMAP, and Leiden clustering for downstream analysis.
• Use Case: Quickly process raw 10x Genomics data into a ready-to-analyze AnnData object, saving researchers from writing extensive boilerplate code.

Quick Start

Run the single-cell preprocessing skill on the provided PBMC3k demo data.