├── .gitignore ├── LICENSE ├── README.md ├── _deprecated ├── TORCHmodels │ ├── compositeModel.lua │ ├── dataPrep │ │ ├── data4prediction.py │ │ ├── data4predictionYAC.py │ │ └── data4trainng.py │ ├── getData.lua │ ├── getDataPred.lua │ ├── models │ │ ├── DSmodel.lua │ │ ├── MSmodel.lua │ │ ├── NSmodel.lua │ │ ├── RSmodel.lua │ │ └── TFmodel.lua │ ├── predictModel.lua │ ├── protocols.txt │ ├── runall.lua │ ├── submit.sh │ ├── testModel.lua │ ├── testScript.lua │ ├── trainModel.lua │ └── transferModules.lua ├── config_enhancers.json ├── config_ms.json ├── config_ts.json ├── dylanTest.py ├── get_regions_from_ucsc.sh ├── old_configurations.json ├── old_io_tools.py ├── old_main.py ├── parse_gff3.py ├── roman.py └── shm.py ├── dev ├── Tutorial_1.ipynb ├── fiddle_cycle.py └── viz_sequence.py ├── fiddle ├── __init__.py ├── analysis.py ├── architecture.json ├── configurations.json ├── data_prep │ ├── __init__.py │ ├── create_hdf5.py │ ├── data_prep.py │ ├── extract_regions.sh │ └── generate_regions.py ├── guide.ipynb ├── io_tools.py ├── job_submit.sh ├── main.py ├── models.py ├── orchestra_job_submit.sh ├── predictions_visualization.ipynb ├── results_analysis │ ├── bigWigFileManipulations.ipynb │ ├── deepDates.txt │ ├── deepRef.txt │ ├── hdf5_fileManipulations.ipynb │ ├── predictionCheckpoint.ipynb │ ├── suffnecScores.ipynb │ ├── testing_generate_regions.ipynb │ └── testing_h5py.ipynb └── visualization.py └── requirements.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ueser/FIDDLE/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ueser/FIDDLE/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: 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