SingleCellMultiomeEngine

Pure Python single-cell multi-omics integration pipeline.

Features

• scRNA-seq + scATAC-seq joint analysis
• Gene activity score from ATAC peaks
• WNN (Weighted Nearest Neighbor) integration
• CRE linking (peak-gene correlation)
• TF activity inference

Usage

pip install numpy scipy matplotlib
python single_cell_multiome_engine.py

Results (1000 cells, 3000 genes, 50000 peaks)

• 6 cell types: HSC, Progenitor, Monocyte, B cell, T cell, NK cell
• WNN: RNA weight=0.246, ATAC weight=0.753