Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | U | V A allowed (vdjmatch.precursor.ClusterMotif attribute) annotate() (in module vdjmatch.api) (vdjmatch.api.Annotator method) (vdjmatch.match.VdjdbIndex method) annotate_paired() (vdjmatch.api.Annotator method) annotate_pairs() (vdjmatch.match.PairedVdjdbIndex method) annotate_repertoires() (in module vdjmatch) Annotator (class in vdjmatch.api) B background() (in module vdjmatch.evalue) ball_mass() (in module vdjmatch.precursor) best_call() (in module vdjmatch.aggregate) build() (vdjmatch.match.PairedVdjdbIndex class method) (vdjmatch.match.VdjdbIndex class method) build_paired_ref() (in module vdjmatch.evalue.paired) C candidate_schema() (in module vdjmatch.aggregate.candidates) candidates() (in module vdjmatch.aggregate.candidates) (vdjmatch.api.Annotator method) check_junctions() (in module vdjmatch.precursor) cid (vdjmatch.precursor.ClusterMotif attribute) closed_ball_mass() (in module vdjmatch.precursor) ClusterMotif (class in vdjmatch.precursor) coverage_corrected_mass() (in module vdjmatch.precursor) cross_check() (in module vdjmatch.precursor) D donor (vdjmatch.precursor.RecombinationEvent attribute) E empty_hits() (vdjmatch.match.VdjdbIndex method) epitope (vdjmatch.precursor.ClusterMotif attribute) epitope_summary() (in module vdjmatch.aggregate) event_ratio() (in module vdjmatch.precursor) expected_cells() (in module vdjmatch.precursor) F fetch_hf() (in module vdjmatch.db) fetch_latest() (in module vdjmatch.db) from_frame() (vdjmatch.api.Annotator class method) from_path() (vdjmatch.api.Annotator class method) G gene (vdjmatch.precursor.ClusterMotif attribute) genes (vdjmatch.match.VdjdbIndex property) graded_candidates() (vdjmatch.api.Annotator method) H hits() (vdjmatch.api.Annotator method) I index_for() (vdjmatch.match.VdjdbIndex method) J j (vdjmatch.precursor.ClusterMotif attribute) (vdjmatch.precursor.RecombinationEvent attribute) junction_aa (vdjmatch.precursor.RecombinationEvent attribute) junction_nt (vdjmatch.precursor.RecombinationEvent attribute) K kernel_ladder() (in module vdjmatch.evalue.kernel) key (vdjmatch.precursor.RecombinationEvent property) L ladder_cutoffs() (in module vdjmatch.evalue.kernel) latest() (vdjmatch.api.Annotator class method) length (vdjmatch.precursor.ClusterMotif attribute) load() (in module vdjmatch.db) load_cluster_motifs() (in module vdjmatch.precursor) load_compendium() (in module vdjmatch.precursor) load_estimates() (in module vdjmatch.precursor) load_model() (in module vdjmatch.precursor) load_vdjam() (in module vdjmatch.match) local_rank_evidence() (in module vdjmatch.evalue.local_rank) loci (vdjmatch.api.Annotator property) loo_audit() (in module vdjmatch.match.scoring_audit) M matrix_audit() (in module vdjmatch.match.scoring_audit) module vdjmatch.aggregate vdjmatch.aggregate.candidates vdjmatch.api vdjmatch.cluster vdjmatch.db vdjmatch.evalue vdjmatch.evalue.kernel vdjmatch.evalue.paired vdjmatch.io vdjmatch.io.columns vdjmatch.match vdjmatch.match.scoring_audit vdjmatch.precursor motif_mass() (in module vdjmatch.precursor) N normalize_annotation_input() (in module vdjmatch.io) normalize_query() (in module vdjmatch.io.columns) O observed_mass() (in module vdjmatch.precursor) occupancy() (in module vdjmatch.precursor) overlap() (in module vdjmatch.cluster) overlap_metrics() (in module vdjmatch.cluster) P p_at_least() (in module vdjmatch.precursor) paired_candidates() (vdjmatch.api.Annotator method) paired_frequency() (in module vdjmatch.precursor) paired_scan() (in module vdjmatch.evalue.paired) PairedVdjdbIndex (class in vdjmatch.match) parse_scope() (in module vdjmatch.match) pgen() (in module vdjmatch.precursor) precompute_v_loop_distances() (in module vdjmatch.match.tcrdist) precursor_frequency() (in module vdjmatch.precursor) provenance() (in module vdjmatch.db) pvalue() (in module vdjmatch.evalue.paired) Q query_evalues() (in module vdjmatch.evalue) R ranked_candidates() (vdjmatch.api.Annotator method) read_cell() (in module vdjmatch.io) read_rearrangement() (in module vdjmatch.io) read_tcrvdb() (in module vdjmatch.io) RecombinationEvent (class in vdjmatch.precursor) records_for() (vdjmatch.match.VdjdbIndex method) reference_report (vdjmatch.api.Annotator property) replicated() (in module vdjmatch.db) S search_params() (in module vdjmatch.match) select_kernel() (in module vdjmatch.evalue.kernel) shell_profile() (in module vdjmatch.precursor) size (vdjmatch.precursor.ClusterMotif attribute) species (vdjmatch.precursor.ClusterMotif attribute) summarise() (in module vdjmatch.precursor) summarise_group() (in module vdjmatch.precursor) U unified_candidates() (vdjmatch.api.Annotator method) union_mass() (in module vdjmatch.precursor) unseen_junctions() (in module vdjmatch.precursor) V v (vdjmatch.precursor.ClusterMotif attribute) (vdjmatch.precursor.RecombinationEvent attribute) validate_counts() (in module vdjmatch.io.columns) vdjbet_motif_scores() (in module vdjmatch.match.motifs) VdjdbIndex (class in vdjmatch.match) vdjmatch.aggregate module vdjmatch.aggregate.candidates module vdjmatch.api module vdjmatch.cluster module vdjmatch.db module vdjmatch.evalue module vdjmatch.evalue.kernel module vdjmatch.evalue.paired module vdjmatch.io module vdjmatch.io.columns module vdjmatch.match module vdjmatch.match.scoring_audit module vdjmatch.precursor module version() (vdjmatch.api.Annotator class method)