API for JakobPedersenLab/dreams
Deep Read-level Error Model for Sequencing data
| Global functions | |
|---|---|
| bed_to_granges | Man page Source code |
| calc_string_entropy_k_mer | Man page Source code |
| call_cancer | Man page Source code |
| call_cancer_indels | Man page Source code |
| call_mutations | Man page Source code |
| call_mutations_indels | Man page Source code |
| clean_insertions | Man page Source code |
| convert_to_cigar | Man page Source code |
| correct_errors_predictions | Source code |
| correct_errors_predictions_indels | Source code |
| correct_pos_idx_w_cigar | Man page Source code |
| correct_seq | Man page Source code |
| dreams_cc | Man page Source code |
| dreams_cc_indels | Man page Source code |
| dreams_vc | Man page Source code |
| dreams_vc_indels | Man page Source code |
| dreams_vc_parallel | Man page Source code |
| em_objective | Source code Source code |
| em_objective_vc | Source code |
| em_update | Source code Source code |
| em_update_vc | Source code |
| expand_cigar | Man page Source code |
| extract_features_from_bam | Man page Source code |
| extract_features_from_bam_indels | Man page Source code |
| extract_indel_info | Man page Source code |
| extract_mismatch_positions | Man page Source code |
| filter_mismatch_positions | Man page Source code |
| fit_model | Man page Source code |
| fit_model_indels | Man page Source code |
| generate_NN_structure | Man page Source code |
| generate_NN_structure_indels | Man page Source code |
| get_em_parameter_estimates | Source code Source code |
| get_indel_genomic_pos | Man page Source code |
| get_indel_info | Man page Source code |
| get_indel_length | Man page Source code |
| get_indel_length_with_zero | Source code |
| get_indel_type | Man page |
| get_indels_start_positions | Man page Source code |
| get_match_genomic_pos_list | Man page Source code |
| get_mismatch_genomic_pos_list | Man page Source code |
| get_r_CI | Source code |
| get_read_positions_from_BAM | Man page Source code |
| get_read_positions_from_BAM_indels | Man page Source code |
| get_reference_seq | Man page Source code |
| get_starting_values | Source code Source code |
| get_tf_CI | Source code |
| get_tf_estimate_vc | Source code |
| get_training_data | Man page Source code |
| get_training_data_from_bam | Man page Source code |
| get_training_data_from_bam_indel | Man page Source code |
| get_training_data_indels | Man page Source code |
| hardclip_correct_umi_features | Man page Source code |
| limit | Source code Source code |
| load_BAM | Man page Source code |
| log_likelihood | Source code |
| predict_error_rates | Source code |
| predict_error_rates_indels | Source code |
| prepare_em_input | Source code |
| prepare_em_input_indels | Source code |
| prepare_input_layer | Man page Source code |
| prepare_input_layer_indels | Man page Source code |
| prepare_training_data | Man page Source code |
| prepare_training_data_indels | Man page Source code |
| read_mutations_df | Man page Source code |
| remove_hardclips | Man page Source code |
| remove_softclips | Man page Source code |
| run_full_em | Source code Source code |
| run_full_em_vc | Source code |
| run_turbo_em | Source code Source code |
| run_turbo_em_vc | Source code |
| sample_negative_read_positions | Man page Source code |
| sample_negative_read_positions_indels | Man page |
| strand_correct_umi_features | Man page Source code |
| train_dreams_model | Man page Source code |
| train_dreams_model_indels | Man page Source code |
| update_P | Source code |
| update_P_Z | Source code |
| update_r | Source code |
| update_tf | Source code |
