API for GenomeNet/deepG
Deep Learning for Genome Sequence Data
| Global functions | |
|---|---|
| %>% | Man page |
| .onAttach | Source code |
| .onLoad | Source code |
| GenParams | Source code |
| GenTParams | Source code |
| GenVParams | Source code |
| LRstop | Source code |
| ReadOpt | Source code |
| TB_loss_acc | Source code |
| add_dim | Source code |
| add_hparam_list | Source code |
| auc_wrapper | Man page Source code |
| bal_acc_from_cm | Source code |
| balanced_acc_wrapper | Man page Source code |
| check_layer_name | Source code |
| checkpoint_cb | Source code |
| compile_model | Man page Source code |
| compute_gradients | Source code |
| conf_matrix_cb | Man page Source code |
| cosine_similarity | Source code |
| count_gpu | Source code |
| count_nuc | Source code |
| cpcloss | Source code |
| create_dummy_data | Man page Source code |
| create_model_genomenet | Man page Source code |
| create_model_lstm_cnn | Man page Source code |
| create_model_lstm_cnn_multi_input | Man page Source code |
| create_model_lstm_cnn_target_middle | Man page Source code |
| create_model_lstm_cnn_time_dist | Man page Source code |
| create_model_transformer | Man page Source code |
| create_model_twin_network | Man page Source code |
| create_quality_vector | Source code |
| create_x_y_tensors_lm | Source code |
| crispr_sample | Man page |
| csv_to_tensor | Source code |
| dataset_from_gen | Man page Source code |
| deepG | Man page |
| deepG-package | Man page |
| df_to_distribution_matrix | Source code |
| early_stopping_cb | Source code |
| early_stopping_time_cb | Man page Source code |
| ecoli_small | Man page |
| euclidean_distance | Source code |
| evaluate_linear | Man page Source code |
| evaluate_model | Man page Source code |
| evaluate_sigmoid | Man page Source code |
| evaluate_softmax | Man page Source code |
| exp_decay | Man page Source code |
| f1_wrapper | Man page Source code |
| f_reshape | Source code |
| focal_loss_multiclass | Man page Source code |
| function_args_cb | Source code |
| generator_dummy | Man page Source code |
| generator_fasta_label_folder | Man page Source code |
| generator_fasta_label_folder_wrapper | Man page Source code |
| generator_fasta_label_header_csv | Man page Source code |
| generator_fasta_lm | Man page Source code |
| generator_initialize | Man page Source code |
| generator_random | Man page Source code |
| generator_rds | Man page Source code |
| getEpochLR | Source code |
| get_callbacks | Source code |
| get_class_weight | Man page Source code |
| get_cp | Source code |
| get_generator | Man page Source code |
| get_hyper_param | Source code |
| get_layer_names | Source code |
| get_maxlen | Source code |
| get_mc | Source code |
| get_optimizer | Source code |
| get_output_activations | Man page Source code |
| get_pooling_flatten_layer | Source code |
| get_run_name | Source code |
| get_seed | Source code |
| get_start_ind | Man page Source code |
| get_x_index | Source code |
| gradients_stepwise | Source code |
| heatmaps_integrated_grad | Man page Source code |
| hyper_param_model_outside_cb | Source code |
| hyper_param_with_model_cb | Source code |
| input_from_csv | Source code |
| int_to_n_gram | Man page |
| integral_approximation | Source code |
| integrated_gradients | Man page Source code |
| interpolate_seq | Source code |
| layer_aggregate_time_dist_wrapper | Man page Source code |
| layer_cosine_sim_wrapper | Source code |
| layer_euc_dist_wrapper | Source code |
| layer_pos_embedding_wrapper | Man page Source code |
| layer_pos_sinusoid_wrapper | Man page Source code |
| layer_transformer_block_wrapper | Man page Source code |
| load_cp | Man page Source code |
| load_model | Source code |
| load_prediction | Man page Source code |
| log_cb | Source code |
| loss_cl | Man page Source code |
| manage_metrics | Source code |
| maxlencalc | Source code |
| merge_models | Man page Source code |
| model_card_cb | Man page Source code |
| modelstep | Source code |
| n_gram_dist | Man page Source code |
| n_gram_of_matrix | Man page |
| noisy_loss_wrapper | Man page Source code |
| nopatchescalc | Source code |
| one_hot_to_seq | Man page |
| parenthesis | Man page |
| plot_cm | Man page Source code |
| plot_roc | Man page Source code |
| pooling_flatten | Source code |
| pooling_flatten_time_dist | Source code |
| predict_model | Man page Source code |
| predict_model_by_entry | Source code |
| predict_model_by_entry_one_file | Source code |
| predict_model_one_pred_per_entry | Source code |
| predict_model_one_seq | Source code |
| predict_with_n_gram | Man page Source code |
| quality_to_probability | Source code |
| random_seq | Source code |
| read_fasta_fastq | Source code |
| reduce_lr_cb | Source code |
| remove_add_layers | Man page Source code |
| remove_amb_nuc_entries | Source code |
| remove_checkpoints | Man page Source code |
| reorder_masked_lm_lists | Source code |
| reset_states_cb | Man page Source code |
| reshape_input | Man page Source code |
| reshape_tensor | Man page |
| reshape_y_list | Source code |
| resume_training_from_model_card | Man page Source code |
| savechecks | Source code |
| seq_encoding_label | Man page Source code |
| seq_encoding_lm | Man page Source code |
| set_new_run_name | Source code |
| set_optimizer | Source code |
| sgdr | Man page Source code |
| shuffle_batches | Source code |
| shuffle_sample | Source code |
| slice_tensor_lm | Source code |
| split_fasta | Man page |
| start_ind_ignore_amb | Source code |
| start_ind_ignore_amb_single_seq | Source code |
| stepdecay | Man page Source code |
| stridecalc | Source code |
| summarize_states | Man page Source code |
| tensorboard_cb | Source code |
| tensorboard_complete_cb | Source code |
| to_time_dist | Source code |
| train_model | Man page Source code |
| train_model_cpc | Man page Source code |
| validation_after_training_cb | Man page Source code |
