Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z A AA_CLONOTYPE_KEY (in module vdjtools.io.schema) aa_group() (in module vdjtools.signature.features) add_locus() (in module vdjtools.io.schema) AIRR AIRR_COLUMNS (in module vdjtools.sc.airr) AIRR_FUNCTIONAL_COLUMNS (in module vdjtools.io.schema) ALICE alice() (in module vdjtools.cli) (in module vdjtools.overlap.alice) allele AMINO_ACIDS (in module vdjtools.signature.layout) anchor annotate() (in module vdjtools.model.stitch) annotate_reads() (in module vdjtools.model.data) apply() (in module vdjtools.signature.corpus) (in module vdjtools.signature.transform) apply_vj_correction() (in module vdjtools.preprocess.batch) arcsine transform arcsine() (in module vdjtools.signature) (in module vdjtools.signature.transform) arda_full_germline() (in module vdjtools.model.reference) arda_masks() (in module vdjtools.model.infer) ARDA_STATUS (in module vdjtools.sc.read) assert_parseable() (in module vdjtools.signature.features) assert_resolvable() (in module vdjtools.io.schema) assign_singleton_ids() (in module vdjtools.sc.cluster_eval) association() (in module vdjtools.biomarker.association) asymptotic_diversity() (in module vdjtools.stats.inext) attained_coverage() (in module vdjtools.signature.signature) augment_from_oracle() (in module vdjtools.model.infer) B bayes_bf() (in module vdjtools.biomarker.stats) bayes_logodds() (in module vdjtools.biomarker.stats) bayes_net_dot() (in module vdjtools.model.analyze) best_aa_scenarios() (in module vdjtools.model.native) best_aa_scenarios_batch() (in module vdjtools.model.native) best_scenario() (in module vdjtools.model.viterbi) binary() (in module vdjtools.biomarker.condition) bounds_for() (in module vdjtools.signature.corpus) build_all() (in module vdjtools.model.data) BUILD_DEFAULTS (in module vdjtools.model.data) build_matrices() (in module vdjtools.signature.corpus) build_model() (in module vdjtools.model.data) build_pools() (in module vdjtools.signature.corpus) builder_version (vdjtools.model.schema.Manifest attribute) bundled_names() (in module vdjtools.signature.corpus) bundled_path() (in module vdjtools.signature.corpus) C C-star call_alleles() (in module vdjtools.model.infer) capture_paired_test() (in module vdjtools.dynamics.capture) capture_rates() (in module vdjtools.dynamics.capture) capture_test() (in module vdjtools.dynamics.capture) categorical() (in module vdjtools.biomarker.condition) CDR3 cdr3_nt (vdjtools.model.viterbi.Scenario attribute) chain_multiplicity() (in module vdjtools.sc.pair) chain_type (vdjtools.model.model.Model property) (vdjtools.model.schema.Manifest attribute) channel Channel (class in vdjtools.signature) (class in vdjtools.signature.layout) channel_columns() (in module vdjtools.signature) (in module vdjtools.signature.layout) channel_table() (in module vdjtools.signature.layout) channels() (in module vdjtools.signature) (in module vdjtools.signature.layout) chao1() (in module vdjtools.stats.diversity) chao_e() (in module vdjtools.stats.diversity) check_model() (in module vdjtools.model.check) chi2_p() (in module vdjtools.biomarker.stats) clamp() (in module vdjtools.signature.corpus) CLASSES (in module vdjtools.dynamics.paired) clon_group() (in module vdjtools.signature.features) clonality clone size clonotype clr clr() (in module vdjtools.signature) (in module vdjtools.signature.transform) cluster_eval() (in module vdjtools.sc.cluster_eval) cluster_samples() (in module vdjtools.overlap.cluster) cmh() (in module vdjtools.biomarker.stats) codon_options() (in module vdjtools.model.viterbi) cohort COHORT (in module vdjtools.signature.corpus) cohort_bands() (in module vdjtools.signature.corpus) COHORT_QS (in module vdjtools.signature.corpus) collapse_alleles() (in module vdjtools.model.collapse) collapse_duplicates() (in module vdjtools.io.schema) column_names() (in module vdjtools.io.schema) COLUMNS (in module vdjtools.io.schema) columns() (vdjtools.signature.Corpus method) (vdjtools.signature.corpus.Corpus method) (vdjtools.signature.layout.RawGroup method) (vdjtools.signature.RawGroup method) compare_entropy() (in module vdjtools.model.analyze) compare_models() (in module vdjtools.model.analyze) compare_net_dot() (in module vdjtools.model.analyze) compare_pgen() (in module vdjtools.model.score) compare_usage() (in module vdjtools.model.analyze) CONSENSUS_COUNT (in module vdjtools.sc.airr) converged (vdjtools.model.infer.InferenceReport attribute) convert() (in module vdjtools.cli) cooccurrence() (in module vdjtools.biomarker.cooccurrence) copula_uniforms() (in module vdjtools.signature.corpus) CORPORA_INDEX (in module vdjtools.signature.corpus) corpora_index() (in module vdjtools.signature.corpus) corpus Corpus (class in vdjtools.signature) (class in vdjtools.signature.corpus) corpus_cache_dir() (in module vdjtools.signature.corpus) corpus_meta() (in module vdjtools.signature.corpus) corpus_plan() (in module vdjtools.signature.corpus) CORPUS_RELEASE (in module vdjtools.signature.corpus) correct() (in module vdjtools.preprocess.correct) correct_vj() (in module vdjtools.cli) correct_vj_usage() (in module vdjtools.preprocess.batch) coverage coverage() (in module vdjtools.stats.inext) coverage_of() (in module vdjtools.signature.features) cut_segment() (in module vdjtools.model.reference) cut_segment_d() (in module vdjtools.model.reference) D d50 d50() (in module vdjtools.stats.diversity) d_call (vdjtools.model.viterbi.Scenario attribute) d_end (vdjtools.model.viterbi.Scenario attribute) d_start (vdjtools.model.viterbi.Scenario attribute) decontaminate() (in module vdjtools.preprocess.decontaminate) DEFAULT_COMPONENTS (in module vdjtools.signature.corpus) DEFAULT_KEY (in module vdjtools.dynamics.paired) (in module vdjtools.overlap.cluster) (in module vdjtools.overlap.metrics) (in module vdjtools.overlap.track) DEFAULT_PROPERTIES (in module vdjtools.features.physchem) DEFAULT_Q (in module vdjtools.overlap.alice) DEFAULT_SIZE (in module vdjtools.signature.corpus) DELETION (vdjtools.model.events.EventKind attribute) DELETION_2D (vdjtools.model.events.EventKind attribute) DELETION_ENDS (in module vdjtools.model.check) depth_group() (in module vdjtools.signature.features) DEPTH_SPREAD (in module vdjtools.signature.corpus) depth_spread_of() (in module vdjtools.signature.corpus) DINUCLEOTIDE (vdjtools.model.events.EventKind attribute) direction() (in module vdjtools.biomarker.stats) dispersion div_group() (in module vdjtools.signature.features) diversity() (in module vdjtools.cli) (in module vdjtools.model.score) diversity_cohort() (in module vdjtools.stats.diversity) diversity_stats() (in module vdjtools.stats.diversity) downsample() (in module vdjtools.cli) (in module vdjtools.preprocess.downsample) downsampling draw_one() (in module vdjtools.signature.corpus) draw_plan() (in module vdjtools.signature.corpus) draw_pool() (in module vdjtools.signature.corpus) draw_sample() (in module vdjtools.signature.corpus) draw_sizes() (in module vdjtools.signature.corpus) duplicate_keys() (in module vdjtools.io.schema) dynamics() (in module vdjtools.cli) E effective dimension efron_thisted() (in module vdjtools.stats.diversity) elapsed_s (vdjtools.model.infer.InferenceReport attribute) emitted_loci (vdjtools.signature.layout.RawGroup property) (vdjtools.signature.RawGroup property) enforce_dj_order() (in module vdjtools.model.infer) entropy_table() (in module vdjtools.model.analyze) error_rate (vdjtools.model.schema.Manifest attribute) estimable() (in module vdjtools.signature.features) estimate_d() (in module vdjtools.stats.inext) estimate_neff() (in module vdjtools.dynamics.paired) Event (class in vdjtools.model.events) EventKind (class in vdjtools.model.events) events (vdjtools.model.schema.Manifest attribute) expanded clone expansion_test() (in module vdjtools.dynamics.expansion) extend_alleles() (in module vdjtools.model.infer) extract_vdj() (in module vdjtools.io.convert) F fdr_bh() (in module vdjtools.biomarker.stats) feat_lf (vdjtools.biomarker.association.FeatureFrame attribute) feats() (in module vdjtools.signature) (in module vdjtools.signature.layout) FeatureFrame (class in vdjtools.biomarker.association) featuriser() (in module vdjtools.signature.corpus) fetch_artifact() (in module vdjtools.signature.corpus) fetch_fastq() (in module vdjtools.model.data) fill_row() (in module vdjtools.signature.corpus) filter_() (in module vdjtools.cli) filter_by_sample() (in module vdjtools.preprocess.filter) filter_frequency() (in module vdjtools.preprocess.filter) filter_functional() (in module vdjtools.preprocess.filter) filter_functional_genes() (in module vdjtools.preprocess.filter) filter_length() (in module vdjtools.preprocess.filter) filter_productive() (in module vdjtools.preprocess.filter) filter_segment() (in module vdjtools.preprocess.filter) finished_at (vdjtools.model.infer.InferenceReport attribute) fisher_association() (in module vdjtools.biomarker.fisher) fisher_p() (in module vdjtools.biomarker.stats) fit() (in module vdjtools.signature) (in module vdjtools.signature.corpus) fit_cohort() (in module vdjtools.signature.corpus) fit_locus() (in module vdjtools.signature.corpus) fit_matrices() (in module vdjtools.signature.corpus) flag_mispairing() (in module vdjtools.sc.pair) forbidden_dj_pairs() (in module vdjtools.model.reference) free_params() (in module vdjtools.model.score) freq_a (vdjtools.overlap.similarity.SimilarityMatrices attribute) freq_b (vdjtools.overlap.similarity.SimilarityMatrices attribute) from_airr() (in module vdjtools.sc.airr) from_arda() (in module vdjtools.model.io) from_dandelion() (in module vdjtools.sc.dandelion) from_dict() (vdjtools.model.infer.InferenceReport class method) from_germline() (in module vdjtools.model.io) from_json() (vdjtools.model.schema.Manifest class method) from_olga() (in module vdjtools.model.io) from_scirpy() (in module vdjtools.sc.anndata) functional gene functional_diversity() (in module vdjtools.stats.functional) fuzzy_overlap() (in module vdjtools.overlap.fuzzy) fuzzy_overlap_metrics() (in module vdjtools.overlap.fuzzy) G gene gene-level call GENE_CHOICE (vdjtools.model.events.EventKind attribute) gene_marginal() (in module vdjtools.model.analyze) gene_masks() (in module vdjtools.model.infer) gene_to_allele() (in module vdjtools.model.native) gene_tv (vdjtools.model.infer.InferenceReport attribute) gene_vocab() (in module vdjtools.signature) (in module vdjtools.signature.features) generate() (in module vdjtools.cli) (in module vdjtools.model.generate) generation model genomic (vdjtools.model.model.Model attribute) germline germline_boundary() (in module vdjtools.model.boundary) GERMLINE_REQUIRED (in module vdjtools.model.reference) given (vdjtools.model.events.Event attribute) H has_nt_resolution() (in module vdjtools.io.schema) has_tandem() (in module vdjtools.model.dd) Hill number hla_alleles() (in module vdjtools.biomarker.condition) holes homogeneity() (in module vdjtools.sc.cluster_eval) I idcols (vdjtools.biomarker.association.FeatureFrame attribute) incidence inext() (in module vdjtools.stats.inext) inext_batch() (in module vdjtools.stats.inext) inext_coverage() (in module vdjtools.stats.inext) infer() (in module vdjtools.model.infer) infer_frame() (in module vdjtools.model.infer) infer_native() (in module vdjtools.model.infer) infer_nt() (in module vdjtools.model.viterbi) infer_nt_bruteforce() (in module vdjtools.model.viterbi) infer_nt_many() (in module vdjtools.model.native) InferenceReport (class in vdjtools.model.infer) ingest_cohort() (in module vdjtools.io.cohort) init (vdjtools.model.infer.InferenceReport attribute) INS_LENGTH (vdjtools.model.events.EventKind attribute) inverse_purity() (in module vdjtools.sc.cluster_eval) inverse_simpson() (in module vdjtools.stats.diversity) iso_group() (in module vdjtools.signature.features) isotype ISOTYPES (in module vdjtools.signature.features) iter_samples() (in module vdjtools.io.batch) J j_call (vdjtools.model.viterbi.Scenario attribute) j_start (vdjtools.model.viterbi.Scenario attribute) JITTER (in module vdjtools.preprocess.join) join_samples() (in module vdjtools.preprocess.join) junction JUNCTION (in module vdjtools.sc.airr) K k (vdjtools.signature.Corpus property) (vdjtools.signature.corpus.Corpus property) kernel (vdjtools.overlap.similarity.SimilarityMatrices attribute) KEY_SETS (in module vdjtools.preprocess.pool) keys_a (vdjtools.overlap.similarity.SimilarityMatrices attribute) keys_b (vdjtools.overlap.similarity.SimilarityMatrices attribute) kind (vdjtools.model.events.Event attribute) kmer_cohort() (in module vdjtools.features.kmer) kmer_group() (in module vdjtools.signature.features) KMER_K (in module vdjtools.signature.layout) kmer_profile() (in module vdjtools.features.kmer) L ladder_draw() (in module vdjtools.signature.corpus) len_group() (in module vdjtools.signature.features) list_bundled() (in module vdjtools.model.bundled) load() (vdjtools.model.model.Model class method) (vdjtools.signature.Corpus class method) (vdjtools.signature.corpus.Corpus class method) load_bundled() (in module vdjtools.model.bundled) load_full_vj_germline() (in module vdjtools.model.reference) load_germline() (in module vdjtools.model.reference) load_model() (in module vdjtools.model.io) load_prepared() (in module vdjtools.model.data) load_property_table() (in module vdjtools.features.physchem) LOCI (in module vdjtools.model.bundled) (in module vdjtools.signature.layout) locus (vdjtools.model.model.Model property) (vdjtools.model.schema.Manifest attribute) locus_matrix() (in module vdjtools.signature.corpus) locus_of() (in module vdjtools.io.schema) LOCUS_PAIR_TO_LOCI (in module vdjtools.sc.pair) LocusFit (class in vdjtools.signature.corpus) log10() (in module vdjtools.signature) (in module vdjtools.signature.transform) log1p() (in module vdjtools.signature) (in module vdjtools.signature.transform) logit() (in module vdjtools.signature) (in module vdjtools.signature.transform) loglik (vdjtools.model.infer.InferenceReport attribute) M MAD MAD_TO_SD (in module vdjtools.signature.corpus) Manifest (class in vdjtools.model.schema) manifest (vdjtools.model.model.Model attribute) map_samples() (in module vdjtools.io.batch) margin (vdjtools.model.viterbi.Scenario property) marginals_frame() (in module vdjtools.model.io) max_iter (vdjtools.model.infer.InferenceReport attribute) MAX_JUNCTION_AA (in module vdjtools.preprocess.filter) max_reachable_trim() (in module vdjtools.model.check) metaclonotype metaclonotypes() (in module vdjtools.biomarker.metaclonotype) MIN_JUNCTION_AA (in module vdjtools.preprocess.filter) MIN_SPREAD (in module vdjtools.signature.corpus) Model (class in vdjtools.model.model) model_build() (in module vdjtools.cli) model_check() (in module vdjtools.cli) model_compare() (in module vdjtools.cli) model_compare_pgen() (in module vdjtools.cli) model_diversity() (in module vdjtools.cli) model_entropy() (in module vdjtools.cli) model_export() (in module vdjtools.cli) model_extend() (in module vdjtools.cli) model_fingerprint() (in module vdjtools.signature.corpus) model_fit() (in module vdjtools.model.score) model_learn() (in module vdjtools.cli) model_list() (in module vdjtools.cli) model_log() (in module vdjtools.cli) model_loglik() (in module vdjtools.cli) model_net() (in module vdjtools.cli) MODEL_READS_REPO (in module vdjtools.model.data) model_rescale() (in module vdjtools.cli) model_template() (in module vdjtools.cli) model_version (vdjtools.model.schema.Manifest attribute) models() (in module vdjtools.cli) MODES (in module vdjtools.signature.corpus) module vdjtools vdjtools.biomarker.association vdjtools.biomarker.condition vdjtools.biomarker.cooccurrence vdjtools.biomarker.fisher vdjtools.biomarker.metaclonotype vdjtools.biomarker.stats vdjtools.cli vdjtools.dynamics.capture vdjtools.dynamics.expansion vdjtools.dynamics.groups vdjtools.dynamics.paired vdjtools.features.kmer vdjtools.features.physchem vdjtools.io.batch vdjtools.io.cohort vdjtools.io.convert vdjtools.io.read vdjtools.io.schema vdjtools.model.analyze vdjtools.model.boundary vdjtools.model.bundled vdjtools.model.check vdjtools.model.collapse vdjtools.model.data vdjtools.model.dd vdjtools.model.events vdjtools.model.generate vdjtools.model.infer vdjtools.model.io vdjtools.model.model vdjtools.model.native vdjtools.model.pgen vdjtools.model.reference vdjtools.model.schema vdjtools.model.score vdjtools.model.stitch vdjtools.model.viterbi vdjtools.overlap.alice vdjtools.overlap.cluster vdjtools.overlap.fuzzy vdjtools.overlap.metrics vdjtools.overlap.similarity vdjtools.overlap.tcrnet vdjtools.overlap.track vdjtools.preprocess.batch vdjtools.preprocess.correct vdjtools.preprocess.decontaminate vdjtools.preprocess.downsample vdjtools.preprocess.filter vdjtools.preprocess.join vdjtools.preprocess.pool vdjtools.sc.airr vdjtools.sc.anndata vdjtools.sc.cluster_eval vdjtools.sc.dandelion vdjtools.sc.pair vdjtools.sc.pgen vdjtools.sc.read vdjtools.signature vdjtools.signature.corpus vdjtools.signature.features vdjtools.signature.layout vdjtools.signature.signature vdjtools.signature.transform vdjtools.stats.diversity vdjtools.stats.functional vdjtools.stats.inext vdjtools.stats.rarefaction vdjtools.stats.spectratype vdjtools.stats.usage mutual_information() (in module vdjtools.model.analyze) N N region n_candidates (vdjtools.model.viterbi.Scenario attribute) N_D (vdjtools.model.events.EventKind attribute) n_eff N_EFF (in module vdjtools.signature.corpus) n_iter (vdjtools.model.infer.InferenceReport attribute) n_scoreable (vdjtools.model.infer.InferenceReport attribute) n_sequences (vdjtools.model.infer.InferenceReport attribute) name (vdjtools.model.events.Event attribute) named block named_columns() (in module vdjtools.signature.layout) named_groups() (in module vdjtools.signature.layout) native (vdjtools.model.infer.InferenceReport attribute) NO_LOCUS (in module vdjtools.signature.layout) normalization_keys() (in module vdjtools.model.schema) normalize() (in module vdjtools.io.schema) normalize_germline() (in module vdjtools.model.reference) normalized_inverse_purity() (in module vdjtools.sc.cluster_eval) normalized_purity() (in module vdjtools.sc.cluster_eval) normalized_shannon_wiener() (in module vdjtools.stats.diversity) O observed_richness() (in module vdjtools.stats.diversity) odds_ratio() (in module vdjtools.biomarker.stats) ORGANISM (in module vdjtools.model.data) organism (vdjtools.model.model.Model property) (vdjtools.model.schema.Manifest attribute) overlap() (in module vdjtools.cli) overlap_metrics() (in module vdjtools.overlap.metrics) overlap_pair() (in module vdjtools.overlap.metrics) P pack() (in module vdjtools.model.native) pair_chains() (in module vdjtools.sc.pair) pair_group() (in module vdjtools.signature.features) paired_pgen() (in module vdjtools.sc.pgen) PAIRS (in module vdjtools.signature.features) pairwise_distances() (in module vdjtools.overlap.cluster) palindrome_max (vdjtools.model.schema.Manifest attribute) parse() (in module vdjtools.signature) (in module vdjtools.signature.layout) PARSEABLE_AA (in module vdjtools.signature.features) parsimony() (in module vdjtools.sc.cluster_eval) PC_BLOCK (in module vdjtools.signature.layout) pc_columns() (in module vdjtools.signature) (in module vdjtools.signature.layout) pchem_group() (in module vdjtools.signature.features) permutation_p() (in module vdjtools.biomarker.stats) Pgen pgen (vdjtools.model.viterbi.Scenario attribute) pgen() (in module vdjtools.cli) pgen_aa() (in module vdjtools.model.native) (in module vdjtools.model.pgen) pgen_aa_batch() (in module vdjtools.model.native) pgen_aa_degenerate() (in module vdjtools.model.native) pgen_aa_degenerate_batch() (in module vdjtools.model.native) pgen_frame() (in module vdjtools.model.score) pgen_nt() (in module vdjtools.model.native) (in module vdjtools.model.pgen) pgen_nt_batch() (in module vdjtools.model.native) pgen_spectrum() (in module vdjtools.model.score) pgen_summary() (in module vdjtools.model.score) physchem_profile() (in module vdjtools.features.physchem) poisson_capture() (in module vdjtools.dynamics.capture) pool() (in module vdjtools.cli) POOL_CHUNKS (in module vdjtools.signature.corpus) pool_samples() (in module vdjtools.preprocess.pool) pool_target() (in module vdjtools.signature.corpus) prepare() (in module vdjtools.model.data) (in module vdjtools.model.pgen) prepare_fuzzy_features() (in module vdjtools.biomarker.association) prepare_generation() (in module vdjtools.model.generate) PREPARED_DIR (in module vdjtools.model.data) principal component print_progress() (in module vdjtools.model.infer) productive PRODUCTIVE (in module vdjtools.io.schema) productive_mask() (in module vdjtools.preprocess.filter) public clonotype purity() (in module vdjtools.sc.cluster_eval) push_obs() (in module vdjtools.sc.anndata) Q q_measure() (in module vdjtools.sc.cluster_eval) qc_channel() (in module vdjtools.signature.features) R Rao quadratic entropy rarefaction rarefaction() (in module vdjtools.stats.rarefaction) rarefaction_batch() (in module vdjtools.stats.inext) raw_and_channels() (in module vdjtools.signature) (in module vdjtools.signature.features) raw_columns() (in module vdjtools.signature) (in module vdjtools.signature.layout) raw_groups() (in module vdjtools.signature) (in module vdjtools.signature.layout) RawGroup (class in vdjtools.signature) (class in vdjtools.signature.layout) read read() (in module vdjtools.io.batch) read_10x() (in module vdjtools.sc.read) read_airr() (in module vdjtools.io.read) read_airr_cell() (in module vdjtools.sc.read) read_arda() (in module vdjtools.io.convert) read_arda_cells() (in module vdjtools.sc.read) read_fasta() (in module vdjtools.model.reference) read_germline_fasta() (in module vdjtools.model.reference) read_h5ddl() (in module vdjtools.sc.dandelion) read_imgt() (in module vdjtools.io.convert) read_immunoseq() (in module vdjtools.io.convert) read_metadata() (in module vdjtools.io.batch) read_migec() (in module vdjtools.io.convert) read_mitcr() (in module vdjtools.io.convert) read_mixcr() (in module vdjtools.io.convert) read_parquet() (in module vdjtools.io.read) read_pools() (in module vdjtools.signature.corpus) read_rtcr() (in module vdjtools.io.convert) read_samples() (in module vdjtools.io.batch) read_trust4() (in module vdjtools.io.convert) read_vdjtools() (in module vdjtools.io.read) read_vidjil() (in module vdjtools.io.convert) READS_PER_CLONE (in module vdjtools.signature.corpus) recombination recompute_frequency() (in module vdjtools.io.schema) reconcile_olga() (in module vdjtools.model.reference) register_channel() (in module vdjtools.signature) (in module vdjtools.signature.layout) register_featuriser() (in module vdjtools.signature.corpus) register_raw() (in module vdjtools.signature) (in module vdjtools.signature.layout) render_bayes_net() (in module vdjtools.model.analyze) render_dot() (in module vdjtools.model.analyze) rep (vdjtools.biomarker.association.FeatureFrame attribute) repair_anchors() (in module vdjtools.model.io) repertoire resolve_artifact() (in module vdjtools.signature.corpus) resolve_chains() (in module vdjtools.sc.pair) resolve_duplicates() (in module vdjtools.io.schema) resolve_gene() (in module vdjtools.io.schema) resolve_k() (vdjtools.signature.Corpus method) (vdjtools.signature.corpus.Corpus method) resolve_key() (in module vdjtools.preprocess.pool) resolve_named() (in module vdjtools.signature.layout) resolved_size() (in module vdjtools.signature.corpus) resume() (in module vdjtools.model.infer) reverse_complement() (in module vdjtools.model.reference) richness robust z-score robust_loc_scale() (in module vdjtools.signature.corpus) rotation runner_up_pgen (vdjtools.model.viterbi.Scenario attribute) S sample_coverage() (in module vdjtools.stats.inext) SAMPLE_ID (in module vdjtools.io.cohort) sample_stream() (in module vdjtools.signature.corpus) sanitise() (in module vdjtools.signature) (in module vdjtools.signature.features) sanitize_junctions() (in module vdjtools.model.infer) save() (vdjtools.model.model.Model method) (vdjtools.signature.Corpus method) (vdjtools.signature.corpus.Corpus method) save_model() (in module vdjtools.model.io) SC_COLUMNS (in module vdjtools.sc.read) sc_convert() (in module vdjtools.cli) sc_export() (in module vdjtools.cli) sc_pair() (in module vdjtools.cli) sc_pgen() (in module vdjtools.cli) sc_qc() (in module vdjtools.cli) scan_cohort() (in module vdjtools.io.cohort) Scenario (class in vdjtools.model.viterbi) scenario_p (vdjtools.model.viterbi.Scenario attribute) SCHEMA (in module vdjtools.io.schema) SEED (in module vdjtools.signature.corpus) segment_usage() (in module vdjtools.cli) (in module vdjtools.stats.usage) select_candidates() (in module vdjtools.biomarker.association) select_top() (in module vdjtools.preprocess.downsample) set_marginals() (in module vdjtools.model.io) shannon_wiener() (in module vdjtools.stats.diversity) SHM shm_group() (in module vdjtools.signature.features) signature signature_columns() (in module vdjtools.signature) (in module vdjtools.signature.layout) similarity_matrix() (in module vdjtools.overlap.similarity) similarity_overlap() (in module vdjtools.overlap.similarity) SimilarityMatrices (class in vdjtools.overlap.similarity) singleton size_class() (in module vdjtools.dynamics.capture) SIZE_CLASSES (in module vdjtools.dynamics.capture) sniff_format() (in module vdjtools.io.batch) source (vdjtools.model.schema.Manifest attribute) SOURCES (in module vdjtools.model.bundled) sparse (vdjtools.overlap.similarity.SimilarityMatrices attribute) spec() (vdjtools.signature.layout.RawGroup method) (vdjtools.signature.RawGroup method) spec_group() (in module vdjtools.signature.features) spectratype spectratype() (in module vdjtools.cli) (in module vdjtools.stats.spectratype) SPECTRATYPE_LENGTHS (in module vdjtools.signature.layout) STANDARD_AA (in module vdjtools.overlap.metrics) stitch_contig() (in module vdjtools.model.stitch) stitch_frame() (in module vdjtools.model.stitch) stratified() (in module vdjtools.biomarker.condition) strip_allele() (in module vdjtools.io.schema) strip_allele_values() (in module vdjtools.io.schema) support support_of() (in module vdjtools.signature) (in module vdjtools.signature.layout) SUPPORTS (in module vdjtools.signature.layout) synthesize() (in module vdjtools.signature) (in module vdjtools.signature.corpus) SYNTHETIC (in module vdjtools.signature.corpus) T table_columns() (in module vdjtools.model.schema) tables (vdjtools.model.model.Model attribute) tandem D tau (vdjtools.overlap.similarity.SimilarityMatrices attribute) TCRnet tcrnet() (in module vdjtools.cli) (in module vdjtools.overlap.tcrnet) template_source (vdjtools.model.infer.InferenceReport attribute) test_metaclonotypes() (in module vdjtools.dynamics.groups) test_pair() (in module vdjtools.dynamics.paired) to_airr() (in module vdjtools.sc.airr) to_anndata() (in module vdjtools.sc.anndata) to_dandelion() (in module vdjtools.sc.dandelion) to_dd() (in module vdjtools.model.dd) to_dict() (vdjtools.model.infer.InferenceReport method) to_frame() (vdjtools.model.infer.InferenceReport method) to_json() (vdjtools.model.schema.Manifest method) to_scirpy() (in module vdjtools.sc.anndata) to_unified_cdr3aa() (in module vdjtools.io.convert) tol (vdjtools.model.infer.InferenceReport attribute) total_entropy() (in module vdjtools.model.analyze) track_clonotypes() (in module vdjtools.overlap.track) training (vdjtools.model.model.Model attribute) training_frame() (in module vdjtools.model.infer) TRANSFORMS (in module vdjtools.signature.layout) translate() (in module vdjtools.io.convert) (in module vdjtools.model.reference) translate_junctions() (in module vdjtools.io.convert) truncated (vdjtools.model.viterbi.Scenario attribute) U unique_clonotypes() (in module vdjtools.model.data) usage_group() (in module vdjtools.signature.features) V v_call (vdjtools.model.viterbi.Scenario attribute) v_end (vdjtools.model.viterbi.Scenario attribute) v_kmer_c_profile() (in module vdjtools.features.kmer) VALID_AA (in module vdjtools.signature.features) VALID_LOCI (in module vdjtools.sc.read) validate() (vdjtools.model.model.Model method) validate_germline() (in module vdjtools.model.reference) validate_graph() (in module vdjtools.model.events) validate_tables() (in module vdjtools.model.schema) variance_at() (vdjtools.signature.corpus.LocusFit method) vdjtools module vdjtools.biomarker.association module vdjtools.biomarker.condition module vdjtools.biomarker.cooccurrence module vdjtools.biomarker.fisher module vdjtools.biomarker.metaclonotype module vdjtools.biomarker.stats module vdjtools.cli module vdjtools.dynamics.capture module vdjtools.dynamics.expansion module vdjtools.dynamics.groups module vdjtools.dynamics.paired module vdjtools.features.kmer module vdjtools.features.physchem module vdjtools.io.batch module vdjtools.io.cohort module vdjtools.io.convert module vdjtools.io.read module vdjtools.io.schema module vdjtools.model.analyze module vdjtools.model.boundary module vdjtools.model.bundled module vdjtools.model.check module vdjtools.model.collapse module vdjtools.model.data module vdjtools.model.dd module vdjtools.model.events module vdjtools.model.generate module vdjtools.model.infer module vdjtools.model.io module vdjtools.model.model module vdjtools.model.native module vdjtools.model.pgen module vdjtools.model.reference module vdjtools.model.schema module vdjtools.model.score module vdjtools.model.stitch module vdjtools.model.viterbi module vdjtools.overlap.alice module vdjtools.overlap.cluster module vdjtools.overlap.fuzzy module vdjtools.overlap.metrics module vdjtools.overlap.similarity module vdjtools.overlap.tcrnet module vdjtools.overlap.track module vdjtools.preprocess.batch module vdjtools.preprocess.correct module vdjtools.preprocess.decontaminate module vdjtools.preprocess.downsample module vdjtools.preprocess.filter module vdjtools.preprocess.join module vdjtools.preprocess.pool module vdjtools.sc.airr module vdjtools.sc.anndata module vdjtools.sc.cluster_eval module vdjtools.sc.dandelion module vdjtools.sc.pair module vdjtools.sc.pgen module vdjtools.sc.read module vdjtools.signature module vdjtools.signature.corpus module vdjtools.signature.features module vdjtools.signature.layout module vdjtools.signature.signature module vdjtools.signature.transform module vdjtools.stats.diversity module vdjtools.stats.functional module vdjtools.stats.inext module vdjtools.stats.rarefaction module vdjtools.stats.spectratype module vdjtools.stats.usage module verify() (vdjtools.signature.Corpus method) (vdjtools.signature.corpus.Corpus method) vj_spectratype() (in module vdjtools.stats.spectratype) vj_usage() (in module vdjtools.stats.usage) vsig() (in module vdjtools.signature) (in module vdjtools.signature.signature) vsig_cohort() (in module vdjtools.signature) (in module vdjtools.signature.signature) W weight_expr() (in module vdjtools.io.schema) WEIGHTS (in module vdjtools.signature.features) WINSOR_PS (in module vdjtools.signature.corpus) winsorization work_frame() (in module vdjtools.signature) (in module vdjtools.signature.features) write_airr() (in module vdjtools.sc.airr) write_airr_cell() (in module vdjtools.sc.read) write_prepared() (in module vdjtools.model.data) write_screpertoire() (in module vdjtools.sc.airr) Z z_aa (vdjtools.overlap.similarity.SimilarityMatrices attribute) z_ab (vdjtools.overlap.similarity.SimilarityMatrices attribute) z_bb (vdjtools.overlap.similarity.SimilarityMatrices attribute) Zipf law ZIPF_A (in module vdjtools.signature.corpus) zygosity() (in module vdjtools.biomarker.condition)