├── DeepMod_tools ├── cal_EcoliDetPerf.py ├── generate_motif_pos.py ├── hm_cluster_predict.py └── sum_chr_mod.py ├── INSTALL ├── LICENSE ├── README.md ├── bin ├── DeepMod.py └── DeepMod_scripts │ ├── EventTable.py │ ├── MoveTable.py │ ├── __init__.py │ ├── myCom.py │ ├── myDetect.py │ ├── myGetFeatureBasedPos.py │ └── myMultiBiRNN.py ├── docs ├── Description of well-trained models.md ├── Install.md ├── Reproducibility.md ├── Results_explanation.md └── Usage.md ├── setup.py └── train_deepmod ├── na12878_cluster_train_mod-keep_prob0.7-nb25-chr1 ├── Cg.cov5.nb25.data-00000-of-00001 ├── Cg.cov5.nb25.index ├── Cg.cov5.nb25.meta └── checkpoint ├── rnn_conmodA_E1m2wd21_f7ne1u0_4 ├── checkpoint ├── mod_train_conmodA_E1m2wd21_f3ne1u0.data-00000-of-00001 ├── mod_train_conmodA_E1m2wd21_f3ne1u0.index └── mod_train_conmodA_E1m2wd21_f3ne1u0.meta ├── rnn_conmodA_P100wd21_f7ne1u0_4 ├── checkpoint ├── mod_train_conmodA_P100wd21_f3ne1u0.data-00000-of-00001 ├── mod_train_conmodA_P100wd21_f3ne1u0.index └── mod_train_conmodA_P100wd21_f3ne1u0.meta ├── rnn_conmodC_P100wd21_f7ne1u0_4 ├── checkpoint ├── mod_train_conmodC_P100wd21_f3ne1u0.data-00000-of-00001 ├── mod_train_conmodC_P100wd21_f3ne1u0.index └── mod_train_conmodC_P100wd21_f3ne1u0.meta ├── rnn_f7_wd21_chr1to10_4 ├── checkpoint ├── mod_train_f7_wd21_chr1to10.data-00000-of-00001 ├── mod_train_f7_wd21_chr1to10.index └── mod_train_f7_wd21_chr1to10.meta └── rnn_sinmodC_P100wd21_f7ne1u0_4 ├── checkpoint ├── mod_train_sinmodC_P100wd21_f3ne1u0.data-00000-of-00001 ├── mod_train_sinmodC_P100wd21_f3ne1u0.index └── mod_train_sinmodC_P100wd21_f3ne1u0.meta /DeepMod_tools/cal_EcoliDetPerf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/DeepMod/HEAD/DeepMod_tools/cal_EcoliDetPerf.py -------------------------------------------------------------------------------- /DeepMod_tools/generate_motif_pos.py: 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