API for ginnyintifa/PTMscape
| Global functions | |
|---|---|
| PTM_domain_mapping_enrichment | Man page Source code |
| aaindex_feature_extraction | Source code |
| assemble_window_score_cv | Source code |
| assemble_window_score_target | Source code |
| balanced_size_sampling | Source code |
| balanced_size_sampling_after_combining_pos_neg | Source code |
| build_candidate_df | Source code |
| build_candidate_df_no_positive | Source code |
| build_decoy_df | Source code |
| build_pure_decoy_df | Source code |
| build_purest_decoy_df | Source code |
| calculate_MCC | Source code |
| calculate_individual_ptm | Source code |
| calculate_seq_pairs | Source code |
| calculate_seq_pairs_negative | Source code |
| calculate_tbt_negative_ptms | Man page Source code |
| calculate_tbt_positive_ptms | Man page Source code |
| calculate_tbt_single_ptm | Source code |
| combine_all_features | Source code |
| combine_all_features_no_spider | Source code |
| combine_pos_neg | Source code |
| construct_n_fold_cv_without_decoy | Source code |
| create_gglogo_plot | Source code |
| divide_candidate_to_train_test | Source code |
| domain_subcellular_mapping | Source code |
| extract_site_specific_features | Source code |
| extract_site_specific_features_new | Source code |
| generate_feature_t | Man page Source code |
| generate_feature_wp | Man page Source code |
| generate_training_test_data_t | Man page Source code |
| generate_training_test_data_wp | Man page Source code |
| get_3_roc | Source code |
| get_all_candidate | Source code |
| get_all_candidate_no_positive | Source code |
| get_all_decoy | Source code |
| get_all_pure_decoy | Source code |
| get_all_purest_decoy | Source code |
| get_average_weights_of_ten | Source code |
| get_average_weights_of_two | Source code |
| get_base_freq_matrix | Source code |
| get_fasta_multi_lines_seq | Source code |
| get_hist | Source code |
| get_k_keep | Source code |
| get_matrix_all | Source code |
| get_non_redundant | Source code |
| get_pca_plot | Source code |
| get_pca_plot_two | Source code |
| get_phosphoSVM_site | Source code |
| get_plsda_pos_candi | Source code |
| get_plsda_pos_candi_with_score_selection | Source code |
| get_prot_mean_structure | Source code |
| get_pssm_feature | Source code |
| get_score_threshold | Source code |
| get_slice_rest_subset_index | Source code |
| get_spd33_combined | Source code |
| get_structure_average | Source code |
| get_structure_site_specific | Source code |
| get_subset_train_test | Source code |
| get_subset_train_test_no_shuffle | Source code |
| get_subset_train_test_no_shuffle_windows | Source code |
| get_train_test | Source code |
| get_tsne_pos_candi | Source code |
| get_wanted_proteins | Source code |
| get_z_transform | Source code |
| ggbiplot2 | Source code |
| libsvm_formating | Source code |
| libsvm_formating_single | Source code |
| map_domain | Source code |
| map_domain_old | Source code |
| map_domain_subcellular | Source code |
| map_subcellular_location | Source code |
| plot_plsda_for_two_types | Source code |
| plot_plsda_for_two_types_with_score_selection | Source code |
| plot_weights | Source code |
| predict_on_targeted_proteome | Man page |
| predict_on_whole_proteome | Man page Source code |
| predict_with_liblinear | Man page Source code |
| present_prediction_t | Man page Source code |
| present_prediction_wp | Man page Source code |
| process_n_fold_cross_validation | Man page Source code |
| pssm_feature_extraction | Source code |
| pssm_generation | Source code |
| retrieve_domain_all_mod | Source code |
| retrieve_for_each_mod | Source code |
| scale_test | Source code |
| scale_train | Source code |
| scale_train_single | Source code |
| scale_train_test | Source code |
| scale_train_test_single | Source code |
| select_equal_size_candidate_decoy | Source code |
| spider_feature_joining_without_mean | Source code |
| whichpart | Source code |
| window_formation | Source code |
| window_formation_no_positive | Source code |
