LICENSE
MANIFEST.in
README.md
setup.py
HydRa/HydRa2_0_predict.py
HydRa/HydRa_predict.py
HydRa/__init__.py
HydRa/test_data_load.py
HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_menthaBioPlex_STRING.tsv
HydRa/data/Classification_cv_scores_AllRuns_SONAR+_final_Ensemble_17_3_7_3_combined10RBPlist_noSS_menthaBioPlex_STRING.tsv
HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_AddNoSS_trainedWithWholeDataset.xls
HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_noSS_trainedWithWholeDataset.tsv
HydRa/data/Classification_scores_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_trainedWithWholeDataset.tsv
HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv
HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv
HydRa/data/Classification_scores_TrainingWithTheWholeProteinSet_final_model_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv.bk
HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING.tsv
HydRa/data/Classification_scores_reference_cv_HydRa2.0_DNN_SVM_ProteinBERT_menthaBioPlex_STRING_noSS.tsv
HydRa/data/Combined10RBPlist_uniprotID_20190716.txt
HydRa/data/Combined8RBPlist_plusOOPSXRNAXsharedRBPs_uniprotID_20190717.txt
HydRa/data/FromOrelOcclRun_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl
HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_avg_zscores_statistics.pkl
HydRa/data/HydRa2.0_noSS_Occlusion_maps_seqSVM_seqDNN_ProteinBERT_proteinLengthWiseFib_scores_statistics.pkl
HydRa/data/HydRa2.0_proteins_with_RBP_categories_RBPflagCorrected_Nov2021_new.tsv
HydRa/data/HydRa_v4_7_3_Occlusion_maps_seqSVM_seqDNN_scores_statistics.pkl
HydRa/data/STRING_v10.5_uniprot_edgelist_withoutExperimentalData.txt
HydRa/data/SVM_AAC_chi2_alpha0.01_selected_features_From_WholeDataSet_AACname.txt
HydRa/data/SVM_SS_11mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt
HydRa/data/SVM_SS_15mer_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt
HydRa/data/SVM_SeqFeature_table_comined_all_selected_features_From_WholeDataset_12Apr_AACname.txt
HydRa/data/SVM_mer3_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt
HydRa/data/SVM_mer4_chi2_alpha0.01_with_LinearSVC_selected_features_From_WholeDataSet.txt
HydRa/data/mentha20180108_BioPlex2.0_edgelist.txt
HydRa/data/menthaBioPlex_feature_table_combined10RBPlist.xls
HydRa/data/menthaBioPlex_separatedSTRING_feature_table_combined8RBPlistAddingOOPSXRNAX.xls
HydRa/data/protVec_100d_3grams.csv
HydRa/evaluation/ROC_PR_AUC_analysis.py
HydRa/evaluation/__init__.py
HydRa/models/DNN_seq.py
HydRa/models/Sequence_class.py
HydRa/models/__init__.py
HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5
HydRa/pre_trained/CNN_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5
HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_structure.json
HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_model_weights.h5
HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_structure.json
HydRa/pre_trained/DNN_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_model_weights.h5
HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_OOPSXRNAXadded.h5
HydRa/pre_trained/DenseI21_5_autoencoder_2CNN2MaxPool_64filter5_2poollength_first1500aa_withRBPs_noSS_OOPSXRNAXadded.h5
HydRa/pre_trained/SVM_PPI_MB-S_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl
HydRa/pre_trained/SVM_PPI_MB_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pkl
HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_ModelFile.pickle.pkl
HydRa/pre_trained/SVM_seqOnly_trainedWithWholeDataset_menthaBioPlexSTRING_Final_Model_v4_7_3_MenthaBioPlex_STRING_AddingOOPSXRNAXlabels_newSklearn0.22.1_noSS_WithNoSSmodel_ModelFile.pickle.pkl
HydRa/predictions/Occlusion_1D_analysis_2.py
HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124.py
HydRa/predictions/Occlusion_1D_analysis_SONARplus_intrinsic_on_WuhanVirus_20200124_ensScore.py
HydRa/predictions/Occlusion_map.py
HydRa/predictions/Occlusion_map_v2.py
HydRa/predictions/Occlusion_map_v2_HydRa2_0.py
HydRa/predictions/Occlusion_map_v3_HydRa2_0.py
HydRa/predictions/__init__.py
HydRa/preprocessing/Get_All_selected_SVM_features.py
HydRa/preprocessing/PPI_feature_generation.py
HydRa/preprocessing/__init__.py
HydRa/preprocessing/get_SVM_seq_features.py
HydRa/preprocessing/predict_SS.py
HydRa/preprocessing/Feature_generation/AAC_feature_table_generation.py
HydRa/preprocessing/Feature_generation/PPI_feature_generation.py
HydRa/preprocessing/Feature_generation/Secondary_structure_prediction.py
HydRa/preprocessing/Feature_generation/__init__.py
HydRa/preprocessing/Feature_generation/get_PPI_feature_mat_MB_STRING.py
HydRa/preprocessing/Feature_generation/kmer_table_generation.py
HydRa/preprocessing/Feature_generation/run_get_PPI_feature_mat_MB_STRING_addingOOPSXRNAXlabelsV2.py
HydRa/preprocessing/Feature_selection/Feature_selection_for_each_feature_after_chi2Filtering_forFinalTraining.py
HydRa/preprocessing/Feature_selection/__init__.py
HydRa/training/__init__.py
HydRa/training/train_HydRa.py
HydRa/training/train_HydRa2_0.py
HydRa/training/train_and_evaluate_HydRa.py
HydRa/training/train_and_evaluate_HydRa2_0.py
HydRa/training/train_and_evaluate_HydRa_bk.py
hydra_rbp.egg-info/PKG-INFO
hydra_rbp.egg-info/SOURCES.txt
hydra_rbp.egg-info/dependency_links.txt
hydra_rbp.egg-info/entry_points.txt
hydra_rbp.egg-info/requires.txt
hydra_rbp.egg-info/top_level.txt