├── .gitignore ├── LICENSE ├── README.md ├── configs ├── cellxgene_topk_finetune.yaml ├── eval_annotation.yaml ├── eval_annotation_cellxgene.yaml ├── eval_denoising.yaml ├── eval_genepert.yaml ├── eval_integration.yaml └── eval_perturbation.yaml ├── data_info.csv ├── figures └── scdiff.png ├── main.py ├── notebooks ├── fewshot_cta_analysis.ipynb └── gene_pert_perf.ipynb ├── pyproject.toml ├── requirements.txt ├── results └── fewshot_cta.csv ├── run ├── oneshot.sh └── run.sh ├── scdiff ├── __init__.py ├── collate.py ├── config.py ├── data │ ├── __init__.py │ ├── base.py │ ├── cellxgene.py │ ├── denoising.py │ ├── gene_pert.py │ ├── pancreas.py │ ├── pbmc12k.py │ └── perturbation.py ├── evaluate.py ├── ext │ └── gears │ │ ├── __init__.py │ │ ├── data_utils.py │ │ ├── gears.py │ │ ├── inference.py │ │ ├── model.py │ │ ├── pertdata.py │ │ └── utils.py ├── model.py ├── modules │ ├── classifier.py │ ├── diffusion_model │ │ ├── __init__.py │ │ ├── decoder.py │ │ ├── embedder.py │ │ └── encoder.py │ ├── ema.py │ ├── layers │ │ ├── attention.py │ │ ├── basic.py │ │ └── scmodel.py │ └── text.py ├── patches.py ├── typing.py └── utils │ ├── __init__.py │ ├── data.py │ ├── diffusion.py │ ├── misc.py │ └── modules.py ├── scripts ├── data_stats.py └── download_wnb_results.py └── tests └── data └── test_data_util.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OmicsML/scDiff/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OmicsML/scDiff/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OmicsML/scDiff/HEAD/README.md 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