MultiomeIntegrationEngine

Single-cell multiome integration engine for joint RNA+ATAC analysis, weighted nearest neighbor embedding, and cis-regulatory element linking.

Features

• Joint RNA and ATAC-seq data integration and QC
• Weighted nearest neighbor (WNN) multi-modal embedding
• Gene activity score computation from chromatin accessibility
• Cis-regulatory element (CRE) to gene linking
• Regulatory potential scoring and transcription factor motif analysis

Results

3000 cells; RNA weight=0.944; 100 CREs; RNA concordance=0.908

Usage

pip install numpy scipy matplotlib
python multiome_integration_engine.py

Tags

gene-activity, wnn, chromatin-gene-linking, regulatory-potential