├── BPCA ├── BPCA_dostep.m ├── BPCA_initmodel.m ├── BPCA_plotM.m ├── BPCAfill.m ├── MAGPIE_fill.m └── readme.md ├── LICENSE ├── data ├── annotation_database │ ├── GDI.txt │ ├── Lof.txt │ ├── RVIS.txt │ ├── amino_acid.csv │ ├── blosum.csv │ └── master38.chromhmm.bedg.tar.gz ├── datasets │ ├── acmg_guided.csv │ ├── denovo.csv │ ├── orthogonal.csv │ ├── test.csv │ └── train.csv ├── output │ └── spliceai │ │ └── hg38.fa.fai └── result │ ├── ClinVar_VUS.csv │ ├── MAGPIE.model │ ├── openFE.features │ └── selection.csv ├── download.sh ├── magpie.sh ├── magpie.yml ├── python ├── __pycache__ │ ├── annotation.cpython-39.pyc │ ├── data_process.cpython-39.pyc │ ├── predict.cpython-39.pyc │ ├── train.cpython-39.pyc │ ├── utils.cpython-39.pyc │ └── visualization.cpython-39.pyc ├── annotation.py ├── data_process.py ├── magpie.py ├── predict.py ├── train.py ├── utils.py └── visualization.py ├── readme.md ├── requirements.txt └── spliceai.yml /BPCA/BPCA_dostep.m: 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