├── .gitignore ├── ChromaFold - Visualize and Evaluate.ipynb ├── LICENSE ├── README.md ├── checkpoints ├── chromafold_CTCFChIP_fullmodel.pth.tar ├── chromafold_CTCFmotif.pth.tar ├── chromafold_CTCFmotif_noCoaccessibility.pth.tar └── chromafold_noCTCF.pth.tar ├── chromafold.yml ├── chromafold ├── R_env.sh ├── chromafold.yml ├── dataloader.py ├── inference.py ├── model.py ├── model_bulk_only.py ├── testing.py ├── train.py ├── train_bulkOnly.py ├── training_utils.py ├── util_chrom_start.py └── utils.py ├── data_subset ├── atac │ ├── metacell_mask.csv │ ├── tile_500bp_barcode.npy │ ├── tile_500bp_dict_chr19.p │ ├── tile_50bp_barcode.npy │ ├── tile_50bp_dict_chr19.p │ └── tile_pbulk_50bp_dict_chr19.p ├── dna │ └── hg38_ctcf_motif_score_chr19.p └── hic │ └── imr90_zscore_dict_chr19.p ├── preprocessing_pipeline ├── ArchR_preparation.R ├── ReadMe.md ├── fragment_celltype_merge.py ├── fragment_to_input.sh └── scATAC_preparation.py └── process_input ├── Process Input - Hi-C.ipynb ├── Process 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