scientific-scatac-signac

What problem does it solve?

This skill provides an end-to-end pipeline for scATAC-seq analysis using Signac, SnapATAC2, and episcanpy to preprocess data, call peaks, analyze motif enrichment, compute Gene Activity scores, and integrate RNA data for multimodal interpretation.

Core Features & Use Cases

• Preprocessing & QC: Normalize, filter, and prepare scATAC-seq data for downstream analysis.
• Peak Calling & Motif Enrichment: Identify accessible regions and enrich transcription factor motifs.
• Gene Activity & Multimodal Integration: Derive gene activity scores and combine with scRNA-seq for RNA+ATAC analysis; supports WNN-like integration.
• Use Case: A researcher has scATAC-seq and a matching scRNA-seq dataset and wants to cluster cells, interpret regulatory programs, and map regulatory relationships to gene expression.

Quick Start

Run scatac_pipeline with a fragment_file and optional rna_h5ad to execute the full scATAC-seq integration pipeline.