Index

A

activation (deeprm.model.deeprm_model.ResNetBlock attribute) add_arguments() (in module deeprm.inference.inference) (in module deeprm.inference.inference_preprocess) (in module deeprm.inference.inference_preprocess_python) (in module deeprm.inference.pileup_deeprm) (in module deeprm.qc.inspect_alignment) (in module deeprm.qc.inspect_block) (in module deeprm.qc.inspect_run) (in module deeprm.train.train) (in module deeprm.train.train_compile) (in module deeprm.train.train_preprocess)

assign_block_id() (in module deeprm.train.train_preprocess)

B

bed_formatter() (in module deeprm.inference.pileup_deeprm) BinaryClassDatasetIterator (class in deeprm.train.train_dataloader) block_len (deeprm.model.deeprm_model.TransformerModel attribute) block_score_distribution() (in module deeprm.qc.inspect_block)

bn1 (deeprm.model.deeprm_model.ResNetBlock attribute) bn2 (deeprm.model.deeprm_model.ResNetBlock attribute) bn3 (deeprm.model.deeprm_model.ResNetBlock attribute) bq_plot() (in module deeprm.qc.inspect_block)

C

check_torch_available() (in module deeprm.utils.check_deps) chunk_save_data() (in module deeprm.train.train_compile) close() (deeprm.inference.inference_dataloader.NanoporeDatasetIterator method) cnn_encoder (deeprm.model.deeprm_model.TransformerModel attribute) code (deeprm.utils.check_installation.Issue attribute) collate_fn() (in module deeprm.inference.inference_dataloader) collect() (in module deeprm.utils.check_installation) ColorFormatter (class in deeprm.utils.logging) conv1 (deeprm.model.deeprm_model.ResNetBlock attribute)

conv2 (deeprm.model.deeprm_model.ResNetBlock attribute) conv3 (deeprm.model.deeprm_model.ResNetBlock attribute) converter() (deeprm.utils.logging.ColorFormatter method) create_move_token() (in module deeprm.train.train_preprocess) create_segment_len_arr() (in module deeprm.inference.inference_preprocess_python) (in module deeprm.train.train_preprocess) create_src_pad_mask() (deeprm.model.deeprm_model.TransformerModel method) create_target_mask() (deeprm.model.deeprm_model.TransformerModel method) (in module deeprm.train.train_preprocess) cumsum (deeprm.inference.pileup_genomic.TranscriptMapper attribute)

D

d_model (deeprm.model.deeprm_model.TransformerModel attribute) dag_longest_path() (in module deeprm.train.extract_block) datefmt (deeprm.utils.logging.ColorFormatter attribute) deeprm.inference module deeprm.inference.inference module deeprm.inference.inference_dataloader module deeprm.inference.inference_preprocess module deeprm.inference.inference_preprocess_python module deeprm.inference.pileup_deeprm module deeprm.inference.pileup_genomic module deeprm.model module deeprm.model.deeprm_model module deeprm.qc module deeprm.qc.inspect_alignment module deeprm.qc.inspect_block module deeprm.qc.inspect_run module

deeprm.train module deeprm.train.extract_block module deeprm.train.train module deeprm.train.train_compile module deeprm.train.train_dataloader module deeprm.train.train_preprocess module deeprm.utils module deeprm.utils.activations module deeprm.utils.check_deps module deeprm.utils.check_installation module deeprm.utils.logging module deeprm.utils.memory module deeprm.utils.utils module default_msec_format (deeprm.utils.logging.ColorFormatter attribute) default_time_format (deeprm.utils.logging.ColorFormatter attribute) dropout (deeprm.model.deeprm_model.ResNetBlock attribute)

E

ends (deeprm.inference.pileup_genomic.TranscriptMapper attribute) entry() (in module deeprm.utils.check_installation) expand_token_to_segment() (in module deeprm.train.train_preprocess) extract_block() (in module deeprm.train.extract_block)

extract_blocks_from_read_list_mp_worker() (in module deeprm.train.extract_block) extract_cigar_master() (in module deeprm.qc.inspect_alignment) extract_cigar_worker() (in module deeprm.qc.inspect_alignment) extract_move() (in module deeprm.train.train_preprocess) extract_signal_proc() (in module deeprm.train.train_preprocess)

F

find_block_candidates() (in module deeprm.train.extract_block) flatten_seg_len() (deeprm.model.deeprm_model.TransformerModel method) format() (deeprm.utils.logging.ColorFormatter method) formatException() (deeprm.utils.logging.ColorFormatter method) formatMessage() (deeprm.utils.logging.ColorFormatter method)

formatStack() (deeprm.utils.logging.ColorFormatter method) formatTime() (deeprm.utils.logging.ColorFormatter method) forward() (deeprm.model.deeprm_model.PositionalEncoding method) (deeprm.model.deeprm_model.RegressionHead method) (deeprm.model.deeprm_model.ResNetBlock method) (deeprm.model.deeprm_model.TransformerModel method)

G

get_activation_fn() (in module deeprm.utils.activations) get_ed_kmers() (in module deeprm.train.extract_block) get_error_rate_func() (in module deeprm.qc.inspect_alignment) get_ideal_displacement() (in module deeprm.train.extract_block) get_integer_partition() (in module deeprm.train.extract_block) get_kmer_dict() (in module deeprm.train.extract_block)

get_kmer_tuple() (in module deeprm.train.extract_block) get_logger() (in module deeprm.utils.logging) get_min_ideal_displacement_dict() (in module deeprm.train.extract_block) get_mm_tag() (in module deeprm.inference.pileup_deeprm) get_norm_factor() (in module deeprm.inference.inference_preprocess_python) (in module deeprm.train.train_preprocess) grouped_sum() (in module deeprm.inference.pileup_deeprm)

H

hint (deeprm.utils.check_installation.Issue attribute)

I

inference_loop() (in module deeprm.inference.inference) inference_worker() (in module deeprm.inference.inference)

init_weights() (deeprm.model.deeprm_model.RegressionHead method) (deeprm.model.deeprm_model.TransformerModel method) Issue (class in deeprm.utils.check_installation)

K

kmer_embedding (deeprm.model.deeprm_model.TransformerModel attribute)

kmer_size (deeprm.model.deeprm_model.TransformerModel attribute)

L

lengths (deeprm.inference.pileup_genomic.TranscriptMapper attribute) lin_layers (deeprm.model.deeprm_model.RegressionHead attribute)

load_dataset() (in module deeprm.inference.inference_dataloader) (in module deeprm.train.train_dataloader) load_split_data() (in module deeprm.inference.pileup_genomic)

M

main() (in module deeprm.inference.inference) (in module deeprm.inference.inference_preprocess) (in module deeprm.inference.inference_preprocess_python) (in module deeprm.inference.pileup_deeprm) (in module deeprm.qc.inspect_alignment) (in module deeprm.qc.inspect_block) (in module deeprm.qc.inspect_run) (in module deeprm.train.train) (in module deeprm.train.train_compile) (in module deeprm.train.train_preprocess) (in module deeprm.utils.check_installation) main_worker() (in module deeprm.train.train) map() (deeprm.inference.pileup_genomic.TranscriptMapper method) maybe_index_bam() (in module deeprm.utils.utils) md_to_mismatch_arr() (in module deeprm.qc.inspect_alignment) mean_phred() (in module deeprm.inference.inference_preprocess_python) (in module deeprm.utils.utils) merge_modbam_shards() (in module deeprm.inference.pileup_deeprm) message (deeprm.utils.check_installation.Issue attribute) model_type (deeprm.model.deeprm_model.TransformerModel attribute) module deeprm.inference deeprm.inference.inference deeprm.inference.inference_dataloader deeprm.inference.inference_preprocess deeprm.inference.inference_preprocess_python deeprm.inference.pileup_deeprm deeprm.inference.pileup_genomic deeprm.model deeprm.model.deeprm_model deeprm.qc deeprm.qc.inspect_alignment deeprm.qc.inspect_block deeprm.qc.inspect_run deeprm.train deeprm.train.extract_block deeprm.train.train deeprm.train.train_compile deeprm.train.train_dataloader deeprm.train.train_preprocess deeprm.utils deeprm.utils.activations deeprm.utils.check_deps deeprm.utils.check_installation deeprm.utils.logging deeprm.utils.memory deeprm.utils.utils

motif_cdf() (in module deeprm.qc.inspect_block) motif_composition() (in module deeprm.qc.inspect_block) move_to_dwell() (in module deeprm.inference.inference_preprocess_python) (in module deeprm.train.train_preprocess)

N

NanoporeDataLoader (class in deeprm.inference.inference_dataloader) (class in deeprm.train.train_dataloader) NanoporeDataset (class in deeprm.inference.inference_dataloader) (class in deeprm.train.train_dataloader)

NanoporeDatasetIterator (class in deeprm.inference.inference_dataloader) normalise_trim_segment_signal() (in module deeprm.inference.inference_preprocess_python) nucleotide_composition() (in module deeprm.qc.inspect_block)

P

pad_collate() (in module deeprm.train.train_dataloader) pad_signal() (in module deeprm.train.train_compile) parse_bam() (in module deeprm.inference.inference_preprocess_python) parse_pod5() (in module deeprm.inference.inference_preprocess_python) parse_refflat() (in module deeprm.inference.pileup_genomic) parser() (in module deeprm.utils.check_installation) pe (deeprm.model.deeprm_model.PositionalEncoding attribute) pileup_genomic() (in module deeprm.inference.pileup_genomic) plot_boxplot() (in module deeprm.qc.inspect_alignment) plot_kde() (in module deeprm.qc.inspect_alignment) plot_motif() (in module deeprm.qc.inspect_block)

plot_polya_len() (in module deeprm.qc.inspect_run) plot_qual() (in module deeprm.qc.inspect_run) plot_read_len_mrna() (in module deeprm.qc.inspect_run) plot_read_len_oligo() (in module deeprm.qc.inspect_run) plot_violin() (in module deeprm.qc.inspect_block) pos_encoding (deeprm.model.deeprm_model.TransformerModel attribute) PositionalEncoding (class in deeprm.model.deeprm_model) prepare_dataloader() (in module deeprm.train.train) preprocess_pod5() (in module deeprm.train.train_preprocess) process_dwell_bq() (deeprm.model.deeprm_model.TransformerModel method) process_kmer() (deeprm.model.deeprm_model.TransformerModel method) process_signal() (deeprm.model.deeprm_model.TransformerModel method)

R

read_bam_worker() (in module deeprm.qc.inspect_run) regression_head (deeprm.model.deeprm_model.TransformerModel attribute) RegressionHead (class in deeprm.model.deeprm_model)

reinit() (deeprm.train.train_dataloader.NanoporeDataset method) ResNetBlock (class in deeprm.model.deeprm_model) run_inference() (in module deeprm.inference.inference)

S

sample_and_save() (in module deeprm.train.train_compile) sample_and_save_worker() (in module deeprm.train.train_compile) save_npz() (in module deeprm.inference.inference_preprocess_python) (in module deeprm.train.train_preprocess) save_split_data() (in module deeprm.train.train_compile) segment_normalize_signal() (in module deeprm.inference.inference_preprocess_python) (in module deeprm.train.train_preprocess) segmented_signal_to_block() (in module deeprm.inference.inference_preprocess_python) (in module deeprm.train.train_preprocess) seq_len (deeprm.model.deeprm_model.TransformerModel attribute) seq_to_onehot() (in module deeprm.qc.inspect_block) sequence_to_kmer_token() (in module deeprm.train.train_preprocess)

set_epoch() (deeprm.train.train_dataloader.NanoporeDataLoader method) (deeprm.train.train_dataloader.NanoporeDataset method) setup_ddp() (in module deeprm.train.train) severity (deeprm.utils.check_installation.Issue attribute) shm_put_array() (in module deeprm.inference.pileup_deeprm) shm_view() (in module deeprm.inference.pileup_deeprm) shortcut (deeprm.model.deeprm_model.ResNetBlock attribute) signal_embedding (deeprm.model.deeprm_model.TransformerModel attribute) signal_stride (deeprm.model.deeprm_model.TransformerModel attribute) split_block_df() (in module deeprm.train.train_preprocess) start_mem_watchdog() (in module deeprm.utils.memory) starts (deeprm.inference.pileup_genomic.TranscriptMapper attribute) strand (deeprm.inference.pileup_genomic.TranscriptMapper attribute)

T

target_end_idx (deeprm.model.deeprm_model.TransformerModel attribute) target_start_idx (deeprm.model.deeprm_model.TransformerModel attribute) to_device() (in module deeprm.inference.inference) total_len (deeprm.inference.pileup_genomic.TranscriptMapper attribute) train() (deeprm.train.train.Trainer method)

Trainer (class in deeprm.train.train) TranscriptMapper (class in deeprm.inference.pileup_genomic) transformer_encoder (deeprm.model.deeprm_model.TransformerModel attribute) TransformerModel (class in deeprm.model.deeprm_model) trim_scale_segment_signal() (in module deeprm.train.train_preprocess)

U

unit_size (deeprm.model.deeprm_model.TransformerModel attribute)

usesTime() (deeprm.utils.logging.ColorFormatter method)

V

validate_anchor() (in module deeprm.train.extract_block)

W

wait_for_processes() (in module deeprm.inference.inference_preprocess_python) worker() (in module deeprm.inference.pileup_deeprm) (in module deeprm.inference.pileup_genomic)

write_df() (in module deeprm.train.train_preprocess) write_modbam_worker_from_map() (in module deeprm.inference.pileup_deeprm)