Index

A

add_locus() (in module vdjtools.io.schema) AIRR_COLUMNS (in module vdjtools.sc.airr) AIRR_FUNCTIONAL_COLUMNS (in module vdjtools.io.schema) alice() (in module vdjtools.cli) (in module vdjtools.overlap.alice) alphabet_table() (in module vdjtools.features.kmer_space) annotate() (in module vdjtools.model.stitch) annotate_reads() (in module vdjtools.model.data) apply_vj_correction() (in module vdjtools.preprocess.batch)

arcsine() (in module vdjtools.signature) arda_full_germline() (in module vdjtools.model.reference) arda_masks() (in module vdjtools.model.infer) ARDA_STATUS (in module vdjtools.sc.read) assign_singleton_ids() (in module vdjtools.sc.cluster_eval) association() (in module vdjtools.biomarker.association) asymptotic_diversity() (in module vdjtools.stats.inext) attributable (vdjtools.signature.Block attribute) 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_scenario() (in module vdjtools.model.viterbi)

binary() (in module vdjtools.biomarker.condition) Block (class in vdjtools.signature) build_all() (in module vdjtools.model.data) BUILD_DEFAULTS (in module vdjtools.model.data) build_model() (in module vdjtools.model.data) builder_version (vdjtools.model.schema.Manifest attribute)

C

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_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) 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) CLASSES (in module vdjtools.dynamics.paired) clr() (in module vdjtools.signature) cluster_eval() (in module vdjtools.sc.cluster_eval) cluster_samples() (in module vdjtools.overlap.cluster) cmh() (in module vdjtools.biomarker.stats) codes (vdjtools.features.kmer_space.KmerSpace attribute) codon_options() (in module vdjtools.model.viterbi)

collapse_alleles() (in module vdjtools.model.collapse) column_names() (in module vdjtools.io.schema) COLUMNS (in module vdjtools.io.schema) columns() (in module vdjtools.signature) (vdjtools.signature.Block 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) components (vdjtools.features.kmer_space.KmerSpace attribute) CONSENSUS_COUNT (in module vdjtools.sc.airr) converged (vdjtools.model.infer.InferenceReport attribute) convert() (in module vdjtools.cli) cooccurrence() (in module vdjtools.biomarker.cooccurrence) correct() (in module vdjtools.preprocess.correct) correct_vj_usage() (in module vdjtools.preprocess.batch) counts() (vdjtools.features.kmer_space.KmerSpace method) coverage() (in module vdjtools.stats.inext) cut_segment() (in module vdjtools.model.reference) cut_segment_d() (in module vdjtools.model.reference)

D

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_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) DELETION (vdjtools.model.events.EventKind attribute)

DELETION_2D (vdjtools.model.events.EventKind attribute) DELETION_ENDS (in module vdjtools.model.check) describe() (in module vdjtools.signature) DINUCLEOTIDE (vdjtools.model.events.EventKind attribute) direction() (in module vdjtools.biomarker.stats) 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) dynamics() (in module vdjtools.cli)

E

efron_thisted() (in module vdjtools.stats.diversity) elapsed_s (vdjtools.model.infer.InferenceReport attribute) emitted_loci (vdjtools.signature.Block property) enforce_dj_order() (in module vdjtools.model.infer) entropy_table() (in module vdjtools.model.analyze) error_rate (vdjtools.model.schema.Manifest attribute) 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) exempt (vdjtools.signature.Block attribute) 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) FeatureFrame (class in vdjtools.biomarker.association) features (vdjtools.signature.Block attribute) fetch_fastq() (in module vdjtools.model.data) 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_kmer_space() (in module vdjtools.features.kmer_space) flag_mispairing() (in module vdjtools.sc.pair) flank (vdjtools.features.kmer_space.KmerSpace attribute) 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_diversity() (in module vdjtools.stats.functional) fuzzy_overlap() (in module vdjtools.overlap.fuzzy) fuzzy_overlap_metrics() (in module vdjtools.overlap.fuzzy)

G

GENE_CHOICE (vdjtools.model.events.EventKind attribute) gene_marginal() (in module vdjtools.model.analyze) gene_masks() (in module vdjtools.model.infer) gene_tv (vdjtools.model.infer.InferenceReport attribute) generate() (in module vdjtools.cli) (in module vdjtools.model.generate)

genomic (vdjtools.model.model.Model attribute) GERMLINE_REQUIRED (in module vdjtools.model.reference) given (vdjtools.model.events.Event attribute) groups (vdjtools.features.kmer_space.KmerSpace attribute)

H

has_tandem() (in module vdjtools.model.dd)

hla_alleles() (in module vdjtools.biomarker.condition) homogeneity() (in module vdjtools.sc.cluster_eval)

I

idcols (vdjtools.biomarker.association.FeatureFrame attribute) idf (vdjtools.features.kmer_space.KmerSpace attribute) index() (in module vdjtools.signature) 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) 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) 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 (in module vdjtools.sc.airr)

K

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_profile() (in module vdjtools.features.kmer) KmerSpace (class in vdjtools.features.kmer_space)

L

list_bundled() (in module vdjtools.model.bundled) load() (vdjtools.model.model.Model 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_kmer_spaces() (in module vdjtools.features.kmer_space) 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)

loci (vdjtools.signature.Block attribute) locus (vdjtools.model.model.Model property) (vdjtools.model.schema.Manifest attribute) locus_of() (in module vdjtools.io.schema) LOCUS_PAIR_TO_LOCI (in module vdjtools.sc.pair) log10() (in module vdjtools.signature) log1p() (in module vdjtools.signature) logit() (in module vdjtools.signature) loglik (vdjtools.model.infer.InferenceReport attribute) lookup() (vdjtools.features.kmer_space.KmerSpace method)

M

magnitude (vdjtools.signature.Block attribute) magnitude_scale() (in module vdjtools.signature) 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) meta (vdjtools.features.kmer_space.KmerSpace attribute) metaclonotypes() (in module vdjtools.biomarker.metaclonotype) MIN_JUNCTION_AA (in module vdjtools.preprocess.filter) 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_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) 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.kmer_space vdjtools.features.physchem vdjtools.io.batch vdjtools.io.cohort vdjtools.io.convert vdjtools.io.read vdjtools.io.schema vdjtools.model.analyze 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.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_candidates (vdjtools.model.viterbi.Scenario attribute) n_columns (vdjtools.features.kmer_space.KmerSpace property) n_components (vdjtools.features.kmer_space.KmerSpace property) N_D (vdjtools.model.events.EventKind attribute) 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) (vdjtools.signature.Block attribute)

native (vdjtools.model.infer.InferenceReport attribute) 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) paired_pgen() (in module vdjtools.sc.pgen) pairwise_distances() (in module vdjtools.overlap.cluster) palindrome_max (vdjtools.model.schema.Manifest attribute) parse() (in module vdjtools.signature) parsimony() (in module vdjtools.sc.cluster_eval) pattern (vdjtools.features.kmer_space.KmerSpace attribute) pattern_of() (in module vdjtools.features.kmer_space) permutation_p() (in module vdjtools.biomarker.stats) 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_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_samples() (in module vdjtools.preprocess.pool) 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) print_progress() (in module vdjtools.model.infer) PRODUCTIVE (in module vdjtools.io.schema) productive_mask() (in module vdjtools.preprocess.filter) purity() (in module vdjtools.sc.cluster_eval) push_obs() (in module vdjtools.sc.anndata)

Q

q_measure() (in module vdjtools.sc.cluster_eval)

R

rarefaction() (in module vdjtools.stats.rarefaction) rarefaction_batch() (in module vdjtools.stats.inext) 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_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) recompute_frequency() (in module vdjtools.io.schema) reconcile_olga() (in module vdjtools.model.reference) reduced_alphabet() (in module vdjtools.features.kmer_space) reference_z() (in module vdjtools.signature) register() (in module vdjtools.signature) registry() (in module vdjtools.signature) render_bayes_net() (in module vdjtools.model.analyze) render_dot() (in module vdjtools.model.analyze) rep (vdjtools.biomarker.association.FeatureFrame attribute) resolve_chains() (in module vdjtools.sc.pair) resolve_gene() (in module vdjtools.io.schema) resolve_key() (in module vdjtools.preprocess.pool) resume() (in module vdjtools.model.infer) reverse_complement() (in module vdjtools.model.reference) robust_loc_scale() (in module vdjtools.signature) runner_up_pgen (vdjtools.model.viterbi.Scenario attribute)

S

sample_coverage() (in module vdjtools.stats.inext) SAMPLE_ID (in module vdjtools.io.cohort) sanitize_junctions() (in module vdjtools.model.infer) save() (vdjtools.model.model.Model method) save_kmer_spaces() (in module vdjtools.features.kmer_space) 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) 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) sig (vdjtools.signature.Block attribute) similarity_matrix() (in module vdjtools.overlap.similarity) similarity_overlap() (in module vdjtools.overlap.similarity) SimilarityMatrices (class in vdjtools.overlap.similarity) 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) spectratype() (in module vdjtools.cli) (in module vdjtools.stats.spectratype) 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)

T

table_columns() (in module vdjtools.model.schema) tables (vdjtools.model.model.Model attribute) tau (vdjtools.overlap.similarity.SimilarityMatrices attribute) 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) transform() (vdjtools.features.kmer_space.KmerSpace method) (vdjtools.signature.Block method) translate() (in module vdjtools.io.convert) (in module vdjtools.model.reference) truncated (vdjtools.model.viterbi.Scenario attribute)

U

unique_clonotypes() (in module vdjtools.model.data)

V

v_call (vdjtools.model.viterbi.Scenario attribute) v_end (vdjtools.model.viterbi.Scenario attribute) v_genes (vdjtools.features.kmer_space.KmerSpace attribute) v_kmer_c_profile() (in module vdjtools.features.kmer) 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) 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.kmer_space 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.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.stats.diversity module vdjtools.stats.functional module vdjtools.stats.inext module vdjtools.stats.rarefaction module vdjtools.stats.spectratype module vdjtools.stats.usage module vj_spectratype() (in module vdjtools.stats.spectratype) vj_usage() (in module vdjtools.stats.usage) vsig() (in module vdjtools.signature) vsig_cohort() (in module vdjtools.signature)

W

weight_expr() (in module vdjtools.io.schema) 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) zygosity() (in module vdjtools.biomarker.condition)