├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── SCRIP ├── Constants.py ├── __init__.py ├── conf │ ├── GRCh38_refgenes.txt │ ├── GRCm38_refgenes.txt │ ├── __init__.py │ ├── config.py │ └── config.yml ├── enhancement │ ├── __init__.py │ └── enhance.py ├── enrichment │ ├── __init__.py │ ├── bed_generation.py │ ├── calculation.py │ ├── enrich.py │ ├── post_processing.py │ ├── search.py │ ├── utils.py │ └── validation.py ├── imputation │ ├── __init__.py │ └── impute.py ├── index │ ├── __init__py │ └── index.py ├── start.py ├── targets │ ├── __init__.py │ └── target.py └── utilities │ ├── __init__.py │ ├── convert_format.py │ ├── convert_seurat2anndata.py │ └── utils.py ├── docs ├── Makefile ├── _static │ ├── custom.css │ └── img │ │ ├── HSC │ │ ├── HSC_celltype.png │ │ └── HSC_diffmap.png │ │ ├── Organs │ │ ├── Organs_GO.png │ │ └── Organs_heatmap.png │ │ ├── PBMC │ │ ├── PBMC_ATAC_BCL11A.png │ │ ├── PBMC_ATAC_BCL11B.png │ │ ├── PBMC_ATAC_annotation.png │ │ ├── PBMC_RNA_Marker_louvain.png │ │ ├── PBMC_RNA_annotation.png │ │ ├── PBMC_RNA_louvain.png │ │ └── PBMC_RNA_qc.png │ │ ├── Tumors │ │ ├── JUNB_target_vol.png │ │ ├── Tcell_na_ex.png │ │ ├── Tumor_heatmap.png │ │ └── junb_go.png │ │ ├── Workflow.png │ │ └── thumbnail │ │ ├── HSC.png │ │ ├── Organs.png │ │ ├── PBMC.png │ │ └── tumor.png ├── conf.py ├── examples.rst ├── examples │ ├── HSC.rst │ ├── PBMC.rst │ ├── Tumor_microenvironment.rst │ └── fetal_organ.rst ├── index.rst ├── installation.rst ├── make.bat ├── release_notes.rst ├── requirements.txt └── usage.rst ├── others ├── backgroundpeaksCCRE.py └── index_generation.py ├── pyproject.toml ├── setup.py └── test ├── config.sh ├── run.sh └── update.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wanglabtongji/SCRIP/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: 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