Index

A

add_delayed_step() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) add_mutation() (tidymut.core.mutation.MutationSet method) add_mutation_set() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) add_mutation_sets() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) add_reference_sequence() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) add_sequences_to_dataset() (in module tidymut.cleaners.human_domainome_custom_cleaners) AminoAcidMutation (class in tidymut.core.mutation)

AminoAcidMutationSet (class in tidymut.core) (class in tidymut.core.mutation) apply() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) apply_mutation() (tidymut.core.sequence.BaseSequence method) apply_mutations_to_sequences() (in module tidymut.cleaners.basic_cleaners) apply_single_mutation() (in module tidymut.utils.cleaner_workers) artifacts (tidymut.core.Pipeline property) (tidymut.core.pipeline.Pipeline property) assign() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method)

B

back_transcribe() (tidymut.core.RNASequence method) (tidymut.core.sequence.RNASequence method) BaseAlphabet (class in tidymut.core.alphabet)

BaseCleanerConfig (class in tidymut.cleaners.base_config) BaseMutation (class in tidymut.core.mutation) BaseSequence (class in tidymut.core.sequence)

C

clean_human_domainome_dataset() (in module tidymut.cleaners) (in module tidymut.cleaners.human_domainome_cleaner) clean_k50_dataset() (in module tidymut.cleaners) (in module tidymut.cleaners.k50_cleaner) clean_protein_gym_dataset() (in module tidymut.cleaners) (in module tidymut.cleaners.protein_gym_cleaner) CodonMutation (class in tidymut.core.mutation) CodonMutationSet (class in tidymut.core) (class in tidymut.core.mutation) CodonTable (class in tidymut.core) (class in tidymut.core.codon) column_mapping (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute), [1] (tidymut.cleaners.HumanDomainomeCleanerConfig attribute), [1] (tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute), [1] (tidymut.cleaners.K50CleanerConfig attribute), [1] (tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute), [1] (tidymut.cleaners.ProteinGymCleanerConfig attribute), [1] convert_codon_to_amino_acid_sets() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method)

convert_data_types() (in module tidymut.cleaners.basic_cleaners) (in module tidymut.utils.type_converter) convert_data_types_batch() (in module tidymut.utils.type_converter) convert_format_1() (in module tidymut.utils.dataset_builders) convert_format_2() (in module tidymut.utils.dataset_builders) convert_to_boolean() (in module tidymut.utils.type_converter) convert_to_mutation_dataset_format() (in module tidymut.cleaners.basic_cleaners) copy() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) count_by_effect_type() (tidymut.core.AminoAcidMutationSet method) (tidymut.core.mutation.AminoAcidMutationSet method) create_human_domainome_cleaner() (in module tidymut.cleaners) (in module tidymut.cleaners.human_domainome_cleaner) create_k50_cleaner() (in module tidymut.cleaners) (in module tidymut.cleaners.k50_cleaner) create_pipeline() (in module tidymut.core) (in module tidymut.core.pipeline) create_protein_gym_cleaner() (in module tidymut.cleaners) (in module tidymut.cleaners.protein_gym_cleaner)

D

data (tidymut.core.Pipeline property) (tidymut.core.pipeline.Pipeline property) delayed_then() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) DNAAlphabet (class in tidymut.core) (class in tidymut.core.alphabet)

DNASequence (class in tidymut.core) (class in tidymut.core.sequence) drop_na_columns (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute), [1] (tidymut.cleaners.HumanDomainomeCleanerConfig attribute), [1]

E

effect_type (tidymut.core.mutation.AminoAcidMutation property) execute() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method)

extract_and_rename_columns() (in module tidymut.cleaners.basic_cleaners) extract_domain_sequences() (in module tidymut.cleaners.human_domainome_custom_cleaners)

F

filter() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) filter_and_clean_data() (in module tidymut.cleaners.basic_cleaners) filter_by_category() (tidymut.core.mutation.MutationSet method) filter_by_effect_type() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) filter_by_mutation_type() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) filter_by_reference() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) filters (tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute), [1] (tidymut.cleaners.K50CleanerConfig attribute), [1] (tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute), [1] (tidymut.cleaners.ProteinGymCleanerConfig attribute), [1]

find_motif() (tidymut.core.ProteinSequence method) (tidymut.core.sequence.ProteinSequence method) from_dataframe() (tidymut.core.dataset.MutationDataset class method) (tidymut.core.MutationDataset class method) from_dict() (tidymut.cleaners.base_config.BaseCleanerConfig class method) from_json() (tidymut.cleaners.base_config.BaseCleanerConfig class method) from_string() (tidymut.core.mutation.AminoAcidMutation class method) (tidymut.core.mutation.BaseMutation class method) (tidymut.core.mutation.CodonMutation class method) (tidymut.core.mutation.MutationSet class method)

G

get_all_artifacts() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) get_artifact() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) get_conversion_function() (in module tidymut.utils.type_converter) get_data() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) get_delayed_steps_info() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) get_execution_summary() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) get_invalid_chars() (tidymut.core.alphabet.BaseAlphabet method) get_missense_mutations() (tidymut.core.AminoAcidMutationSet method) (tidymut.core.mutation.AminoAcidMutationSet method) get_mutation_at() (tidymut.core.mutation.MutationSet method) get_mutation_categories() (tidymut.core.mutation.MutationSet method) get_mutation_category() (tidymut.core.mutation.AminoAcidMutation method) (tidymut.core.mutation.BaseMutation method) (tidymut.core.mutation.CodonMutation method) get_mutation_count() (tidymut.core.mutation.MutationSet method) get_mutation_set_label() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) get_mutation_set_reference() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) get_nonsense_mutations() (tidymut.core.AminoAcidMutationSet method) (tidymut.core.mutation.AminoAcidMutationSet method)

get_one_letter_code() (tidymut.core.alphabet.ProteinAlphabet method) (tidymut.core.ProteinAlphabet method) get_position_coverage() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) get_positions() (tidymut.core.mutation.MutationSet method) get_positions_set() (tidymut.core.mutation.MutationSet method) get_reference_sequence() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) get_residue() (tidymut.core.ProteinSequence method) (tidymut.core.sequence.ProteinSequence method) get_sorted_by_position() (tidymut.core.mutation.MutationSet method) get_standard_table() (tidymut.core.codon.CodonTable class method) (tidymut.core.CodonTable class method) get_statistics() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) get_step_result() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) get_subsequence() (tidymut.core.sequence.BaseSequence method) get_summary() (tidymut.cleaners.base_config.BaseCleanerConfig method) get_synonymous_mutations() (tidymut.core.AminoAcidMutationSet method) (tidymut.core.mutation.AminoAcidMutationSet method) get_table_by_name() (tidymut.core.codon.CodonTable class method) (tidymut.core.CodonTable class method) get_three_letter_code() (tidymut.core.alphabet.ProteinAlphabet method) (tidymut.core.ProteinAlphabet method)

H

handle_multiple_wt (tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute), [1] (tidymut.cleaners.K50CleanerConfig attribute), [1] (tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute), [1] (tidymut.cleaners.ProteinGymCleanerConfig attribute), [1] has_mutation_at() (tidymut.core.mutation.MutationSet method) has_pending_steps (tidymut.core.Pipeline property) (tidymut.core.pipeline.Pipeline property)

has_stop_codon_mutations() (tidymut.core.AminoAcidMutationSet method) (tidymut.core.mutation.AminoAcidMutationSet method) header_parser (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute) (tidymut.cleaners.HumanDomainomeCleanerConfig attribute) header_parser() (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig method) (tidymut.cleaners.HumanDomainomeCleanerConfig method) HumanDomainomeCleanerConfig (class in tidymut.cleaners) (class in tidymut.cleaners.human_domainome_cleaner)

I

infer_wildtype_sequences() (in module tidymut.cleaners.basic_cleaners) infer_wt_sequence_grouped() (in module tidymut.utils.cleaner_workers) infer_wt_workers (tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute), [1] (tidymut.cleaners.K50CleanerConfig attribute), [1] (tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute), [1] (tidymut.cleaners.ProteinGymCleanerConfig attribute), [1] invert_mutation() (in module tidymut.utils.mutation_converter) invert_mutation_set() (in module tidymut.utils.mutation_converter) is_missense() (tidymut.core.mutation.AminoAcidMutation method) is_multiple_mutations() (tidymut.core.mutation.MutationSet method) is_nonsense() (tidymut.core.mutation.AminoAcidMutation method)

is_single_mutation() (tidymut.core.mutation.MutationSet method) is_start_codon() (tidymut.core.codon.CodonTable method) (tidymut.core.CodonTable method) is_stop_codon() (tidymut.core.codon.CodonTable method) (tidymut.core.CodonTable method) is_synonymous() (tidymut.core.mutation.AminoAcidMutation method) is_valid_char() (tidymut.core.alphabet.BaseAlphabet method) is_valid_sequence() (tidymut.core.alphabet.BaseAlphabet method) is_zero_based (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute), [1] (tidymut.cleaners.HumanDomainomeCleanerConfig attribute), [1] (tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute) (tidymut.cleaners.ProteinGymCleanerConfig attribute)

K

K50CleanerConfig (class in tidymut.cleaners) (class in tidymut.cleaners.k50_cleaner)

L

label_columns (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute), [1] (tidymut.cleaners.HumanDomainomeCleanerConfig attribute), [1] (tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute), [1] (tidymut.cleaners.K50CleanerConfig attribute), [1] (tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute), [1] (tidymut.cleaners.ProteinGymCleanerConfig attribute), [1] list_reference_sequences() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method)

load() (tidymut.core.dataset.MutationDataset class method) (tidymut.core.MutationDataset class method) (tidymut.core.Pipeline class method) (tidymut.core.pipeline.Pipeline class method) load_by_reference() (tidymut.core.dataset.MutationDataset class method) (tidymut.core.MutationDataset class method) load_sequences() (in module tidymut.utils.sequence_io) load_structured_data() (tidymut.core.Pipeline class method) (tidymut.core.pipeline.Pipeline class method)

M

merge() (tidymut.cleaners.base_config.BaseCleanerConfig method) merge_columns() (in module tidymut.cleaners.basic_cleaners) module tidymut tidymut.cleaners tidymut.cleaners.base_config tidymut.cleaners.basic_cleaners tidymut.cleaners.human_domainome_cleaner tidymut.cleaners.human_domainome_custom_cleaners tidymut.cleaners.k50_cleaner tidymut.cleaners.protein_gym_cleaner tidymut.cleaners.protein_gym_custom_cleaners tidymut.core tidymut.core.alphabet tidymut.core.codon tidymut.core.constants tidymut.core.dataset tidymut.core.mutation tidymut.core.pipeline tidymut.core.sequence tidymut.core.types tidymut.utils tidymut.utils.cleaner_workers tidymut.utils.dataset_builders tidymut.utils.mutation_converter tidymut.utils.sequence_io tidymut.utils.type_converter

multiout_step() (in module tidymut.core) (in module tidymut.core.pipeline) mutation_subtype (tidymut.core.mutation.MutationSet property) MutationDataset (class in tidymut.core) (class in tidymut.core.dataset) MutationSet (class in tidymut.core.mutation)

N

normalize_type_conversions() (in module tidymut.utils.type_converter)

num_workers (tidymut.cleaners.base_config.BaseCleanerConfig attribute), [1]

P

parse_custom_delimiter_header() (in module tidymut.utils.sequence_io) parse_fasta() (in module tidymut.utils.sequence_io) parse_ncbi_header() (in module tidymut.utils.sequence_io) parse_simple_header() (in module tidymut.utils.sequence_io) parse_uniprot_header() (in module tidymut.utils.sequence_io) peek() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) Pipeline (class in tidymut.core) (class in tidymut.core.pipeline) pipeline_name (tidymut.cleaners.base_config.BaseCleanerConfig attribute), [1] (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute) (tidymut.cleaners.HumanDomainomeCleanerConfig attribute) (tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute) (tidymut.cleaners.K50CleanerConfig attribute) (tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute) (tidymut.cleaners.ProteinGymCleanerConfig attribute)

pipeline_step() (in module tidymut.core) (in module tidymut.core.pipeline) primary_label_column (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute), [1] (tidymut.cleaners.HumanDomainomeCleanerConfig attribute), [1] (tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute), [1] (tidymut.cleaners.K50CleanerConfig attribute), [1] (tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute), [1] (tidymut.cleaners.ProteinGymCleanerConfig attribute), [1] process_domain_positions() (in module tidymut.cleaners.human_domainome_custom_cleaners) process_workers (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute), [1] (tidymut.cleaners.HumanDomainomeCleanerConfig attribute), [1] ProteinAlphabet (class in tidymut.core) (class in tidymut.core.alphabet) ProteinGymCleanerConfig (class in tidymut.cleaners) (class in tidymut.cleaners.protein_gym_cleaner) ProteinSequence (class in tidymut.core) (class in tidymut.core.sequence)

R

read_dataset() (in module tidymut.cleaners.basic_cleaners) read_protein_gym_data() (in module tidymut.cleaners.protein_gym_custom_cleaners) remove_delayed_step() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) remove_mutation() (tidymut.core.mutation.MutationSet method) remove_mutation_set() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) remove_reference_sequence() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method)

reverse_complement() (tidymut.core.DNASequence method) (tidymut.core.RNASequence method) (tidymut.core.sequence.DNASequence method) (tidymut.core.sequence.RNASequence method) RNAAlphabet (class in tidymut.core) (class in tidymut.core.alphabet) RNASequence (class in tidymut.core) (class in tidymut.core.sequence)

S

save() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) save_artifacts() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) save_by_reference() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) save_structured_data() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) seq_type (tidymut.core.CodonMutationSet property) (tidymut.core.mutation.CodonMutationSet property)

sequence_dict_path (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute), [1] (tidymut.cleaners.HumanDomainomeCleanerConfig attribute), [1] set_mutation_set_label() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) set_mutation_set_reference() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) sort_by_position() (tidymut.core.mutation.MutationSet method) store() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) strict_mode (tidymut.cleaners.base_config.BaseCleanerConfig attribute), [1] structured_data (tidymut.core.Pipeline property) (tidymut.core.pipeline.Pipeline property)

T

then() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) tidymut module tidymut.cleaners module tidymut.cleaners.base_config module tidymut.cleaners.basic_cleaners module tidymut.cleaners.human_domainome_cleaner module tidymut.cleaners.human_domainome_custom_cleaners module tidymut.cleaners.k50_cleaner module tidymut.cleaners.protein_gym_cleaner module tidymut.cleaners.protein_gym_custom_cleaners module tidymut.core module tidymut.core.alphabet module tidymut.core.codon module tidymut.core.constants module tidymut.core.dataset module tidymut.core.mutation module tidymut.core.pipeline module tidymut.core.sequence module tidymut.core.types module

tidymut.utils module tidymut.utils.cleaner_workers module tidymut.utils.dataset_builders module tidymut.utils.mutation_converter module tidymut.utils.sequence_io module tidymut.utils.type_converter module to_amino_acid_mutation() (tidymut.core.mutation.CodonMutation method) to_amino_acid_mutation_set() (tidymut.core.CodonMutationSet method) (tidymut.core.mutation.CodonMutationSet method) to_dataframe() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method) to_dict() (tidymut.cleaners.base_config.BaseCleanerConfig method) to_json() (tidymut.cleaners.base_config.BaseCleanerConfig method) transcribe() (tidymut.core.DNASequence method) (tidymut.core.sequence.DNASequence method) transform() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) translate() (tidymut.core.DNASequence method) (tidymut.core.RNASequence method) (tidymut.core.sequence.DNASequence method) (tidymut.core.sequence.RNASequence method) translate_codon() (tidymut.core.codon.CodonTable method) (tidymut.core.CodonTable method) type (tidymut.core.mutation.AminoAcidMutation property) (tidymut.core.mutation.BaseMutation property) (tidymut.core.mutation.CodonMutation property) type_conversions (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute), [1] (tidymut.cleaners.HumanDomainomeCleanerConfig attribute), [1] (tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute), [1] (tidymut.cleaners.K50CleanerConfig attribute), [1] (tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute), [1] (tidymut.cleaners.ProteinGymCleanerConfig attribute), [1]

V

valid_single_mutation() (in module tidymut.utils.cleaner_workers) validate() (tidymut.cleaners.base_config.BaseCleanerConfig method) (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig method) (tidymut.cleaners.HumanDomainomeCleanerConfig method) (tidymut.cleaners.k50_cleaner.K50CleanerConfig method) (tidymut.cleaners.K50CleanerConfig method) (tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig method) (tidymut.cleaners.ProteinGymCleanerConfig method) (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method) validate_against_references() (tidymut.core.dataset.MutationDataset method) (tidymut.core.MutationDataset method)

validate_all() (tidymut.core.mutation.MutationSet method) validate_config (tidymut.cleaners.base_config.BaseCleanerConfig attribute), [1] validate_mutations() (in module tidymut.cleaners.basic_cleaners) validate_sequence() (tidymut.core.alphabet.BaseAlphabet method) validation_workers (tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute), [1] (tidymut.cleaners.K50CleanerConfig attribute), [1] (tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute), [1] (tidymut.cleaners.ProteinGymCleanerConfig attribute), [1] visualize_pipeline() (tidymut.core.Pipeline method) (tidymut.core.pipeline.Pipeline method)

W

write_fasta() (in module tidymut.utils.sequence_io)