Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X A add() (mir.explain.ChannelBuilder method) align_loci() (in module mir.cohort) allele_to_major() (in module mir.alleles) allele_with_default() (in module mir.alleles) alpha (mir.track.TrajectoryFit attribute) antigen_subset() (in module mir.bench.vdjdb) AntigenMetric (class in mir.bench.metrics) ard_precision (mir.track.TrajectoryFit attribute) attributable (mir.explain.ChannelSpec attribute) B b (mir.repertoire.RandomFourierFeatures attribute) band_embeddings() (in module mir.repertoire) band_frames() (in module mir.repertoire) base (mir.explain.ChannelReport attribute) best (mir.explain.ChannelReport property) betas (mir.ml.diffusion.DiffusionModel attribute) blocks (mir.cohort.LocusAlignment attribute) build() (mir.cohort.LocusAlignment method) (mir.explain.ChannelBuilder method) build_parser() (in module mir.cli) C calibrate_radius() (in module mir.density) centroid_atypicality() (in module mir.repertoire) ChainPreset (class in mir.embedding.presets) channel_drivers() (in module mir.explain) channel_names (mir.track.TrajectoryFit attribute) channel_report() (in module mir.explain) ChannelBuilder (class in mir.explain) ChannelReport (class in mir.explain) channels (mir.explain.ChannelReport attribute) ChannelSpec (class in mir.explain) class_witness() (in module mir.repertoire) clono (mir.repertoire.RepertoireSpace attribute) cluster() (in module mir.bench.metrics) cluster_metrics() (in module mir.bench.metrics) cluster_samples() (in module mir.cohort) code() (mir.ml.train.ForwardEncoder method) codec_losslessness() (in module mir.bench.theory) CodecBundle (class in mir.ml.bundle) cohort_statistics() (in module mir.repertoire) columns() (mir.explain.ChannelSpec method) columns_by_name (mir.explain.ChannelSpec attribute) condition (mir.twin.DonorTwin attribute) contrast_embedding() (in module mir.repertoire) converged (mir.track.TrajectoryFit attribute) correct_batch() (in module mir.repertoire) CorrelationResult (class in mir.bench.theory) cosine_beta_schedule() (in module mir.ml.diffusion) cov (mir.generate.DescriptorDensity attribute) covariate_names (mir.track.TrajectoryFit attribute) cv_auc() (in module mir.bench.eval) cv_cindex() (in module mir.bench.eval) D D (mir.bench.theory.CorrelationResult attribute) d (mir.bench.theory.CorrelationResult attribute) decode() (mir.ml.codec.UnifiedCodec method) (mir.ml.train.InverseDecoder method) decode_metrics() (in module mir.repertoire) delta (mir.explain.ChannelReport attribute) delta_out (mir.explain.ChannelReport attribute) denoise_and_cluster() (in module mir.density) DensitySpace (class in mir.density) depth (mir.repertoire.RarefyResult attribute) depth_report() (in module mir.cohort) depth_threshold() (in module mir.repertoire) DepthThreshold (class in mir.repertoire) descriptor (mir.twin.DonorTwin attribute) DescriptorDensity (class in mir.generate) device (mir.ml.set_encoder.SetEncoderModel attribute) DiffusionMLP (class in mir.ml.diffusion) DiffusionModel (class in mir.ml.diffusion) dim (mir.generate.DescriptorDensity attribute) (mir.repertoire.RandomFourierFeatures property) diversity (mir.repertoire.SampleEmbedding attribute) donor_id (mir.twin.DonorTwin attribute) DonorCohort (class in mir.cohort) DonorTwin (class in mir.twin) E embed() (mir.embedding.tcremp.PairedTCREmp method) (mir.embedding.tcremp.TCREmp method) embedding (mir.repertoire.RarefyResult attribute) encode() (mir.ml.codec.UnifiedCodec method) (mir.ml.train.ForwardEncoder method) encode_indices() (in module mir.ml.tokenize) encode_onehot() (in module mir.ml.tokenize) enriched_mask() (in module mir.density) EnrichmentResult (class in mir.density) epitope (mir.bench.metrics.AntigenMetric attribute) estimate_dbscan_eps() (in module mir.bench.metrics) evolve() (in module mir.generate) (mir.generate.DescriptorDensity method) expected (mir.density.EnrichmentResult attribute) exposure_channel() (in module mir.density) exposure_score() (in module mir.density) F f1 (mir.bench.metrics.AntigenMetric attribute) fit() (mir.generate.DescriptorDensity class method) fit_density_space() (in module mir.density) fit_descriptor_density() (in module mir.generate) fit_distributions() (in module mir.bench.theory) fit_donor_embeddings() (in module mir.cohort) fit_exposure_trajectory() (in module mir.track) fit_exposure_trajectory_from_samples() (in module mir.track) fit_repertoire_space() (in module mir.repertoire) fit_repertoire_spaces() (in module mir.repertoire) fold (mir.density.EnrichmentResult attribute) forward() (mir.ml.decoder.SequenceDecoder method) (mir.ml.diffusion.DiffusionMLP method) (mir.ml.encoder.SequenceEncoder method) (mir.ml.set_encoder.SetEncoder method) forward_encoder() (mir.ml.bundle.CodecBundle method) ForwardEncoder (class in mir.ml.train) fraction_below (mir.repertoire.DepthThreshold attribute) frame() (mir.explain.ChannelReport method) from_defaults() (mir.embedding.tcremp.PairedTCREmp class method) (mir.embedding.tcremp.TCREmp class method) from_file() (mir.embedding.tcremp.TCREmp class method) from_forward() (mir.ml.bundle.CodecBundle class method) from_model() (mir.ml.set_encoder.SetEncoderBundle class method) full (mir.explain.ChannelReport attribute) G gain (mir.explain.ChannelReport property) gamma (mir.track.TrajectoryFit attribute) generate_background() (in module mir.density) GermlineDistances (class in mir.distances.germline) get_preset() (in module mir.embedding.presets) get_resource_path() (in module mir) H has() (mir.distances.germline.GermlineDistances method) held_out_auc() (in module mir.bench.eval) hla_stratified_mmd() (in module mir.repertoire) I identity_pca (mir.cohort.DonorCohort attribute) ids (mir.cohort.LocusAlignment attribute) incidence_biomarkers() (in module mir.cohort) interaction_score (mir.track.TrajectoryFit property) intercept (mir.track.TrajectoryFit attribute) InverseDecoder (class in mir.ml.train) J junction_dissimilarity() (in module mir.bench.theory) junction_dissimilarity_sw() (in module mir.bench.theory) junction_distance_matrix() (in module mir.distances.junction) K kappa (mir.repertoire.DepthThreshold attribute) (mir.track.TrajectoryFit attribute) km_logrank() (in module mir.bench.eval) kmer_matrix() (in module mir.bench.eval) L length_scale (mir.repertoire.RandomFourierFeatures attribute) list_available_prototypes() (in module mir.embedding.prototypes) load() (mir.cohort.DonorCohort class method) (mir.distances.germline.GermlineDistances class method) (mir.ml.bundle.CodecBundle class method) (mir.ml.diffusion.DiffusionModel class method) (mir.ml.set_encoder.SetEncoderBundle class method) (mir.repertoire.RepertoireSpace class method) load_germline_distances() (in module mir.distances.germline) load_prototypes() (in module mir.embedding.prototypes) load_vdjdb() (in module mir.bench.vdjdb) loci (mir.cohort.LocusAlignment attribute) LocusAlignment (class in mir.cohort) log_mass (mir.repertoire.RepertoireDescriptor attribute) log_neff (mir.repertoire.RepertoireDescriptor attribute) loglik_trace (mir.track.TrajectoryFit attribute) M main() (in module mir.cli) make_twins() (in module mir.twin) mask (mir.cohort.LocusAlignment attribute) mass (mir.repertoire.SampleEmbedding attribute) matches_current_prototypes() (mir.ml.bundle.CodecBundle method) matches_prototype_hash() (mir.ml.diffusion.DiffusionModel method) matrix() (mir.distances.germline.GermlineDistances method) mean (mir.generate.DescriptorDensity attribute) (mir.repertoire.RepertoireDescriptor attribute) (mir.repertoire.SampleEmbedding attribute) meta (mir.cohort.DonorCohort attribute) (mir.ml.bundle.CodecBundle attribute) (mir.ml.diffusion.DiffusionModel attribute) (mir.ml.set_encoder.SetEncoderBundle attribute) (mir.repertoire.RepertoireSpace attribute) metrics() (mir.repertoire.RepertoireDescriptor method) (mir.twin.DonorTwin method) mir module mir.aliases module mir.alleles module mir.bench.eval module mir.bench.metrics module mir.bench.theory module mir.bench.vdjdb module mir.cli module mir.cohort module mir.density module mir.distances.germline module mir.distances.junction module mir.embedding.pca module mir.embedding.presets module mir.embedding.prototypes module mir.embedding.tcremp module mir.explain module mir.generate module mir.ml.bundle module mir.ml.codec module mir.ml.decoder module mir.ml.diffusion module mir.ml.encoder module mir.ml.set_encoder module mir.ml.tokenize module mir.ml.train module mir.repertoire module mir.track module mir.twin module missing_mass() (in module mir.repertoire) missingness_report() (in module mir.cohort) (mir.cohort.DonorCohort method) (mir.cohort.LocusAlignment method) mixture_weights() (in module mir.repertoire) mmd_distance() (in module mir.repertoire) mmd_matrix() (in module mir.repertoire) mode (mir.explain.ChannelReport attribute) model (mir.density.DensitySpace attribute) (mir.ml.bundle.CodecBundle attribute) (mir.ml.diffusion.DiffusionModel attribute) (mir.ml.set_encoder.SetEncoderBundle attribute) (mir.ml.set_encoder.SetEncoderModel attribute) module mir mir.aliases mir.alleles mir.bench.eval mir.bench.metrics mir.bench.theory mir.bench.vdjdb mir.cli mir.cohort mir.density mir.distances.germline mir.distances.junction mir.embedding.pca mir.embedding.presets mir.embedding.prototypes mir.embedding.tcremp mir.explain mir.generate mir.ml.bundle mir.ml.codec mir.ml.decoder mir.ml.diffusion mir.ml.encoder mir.ml.set_encoder mir.ml.tokenize mir.ml.train mir.repertoire mir.track mir.twin N n (mir.bench.metrics.AntigenMetric attribute) (mir.bench.theory.CorrelationResult attribute) n_bg (mir.density.EnrichmentResult attribute) n_components (mir.embedding.presets.ChainPreset attribute) n_components_recon (mir.embedding.presets.ChainPreset attribute) n_eff (mir.repertoire.SampleEmbedding attribute) n_features (mir.embedding.tcremp.PairedTCREmp property) (mir.embedding.tcremp.TCREmp property) n_iter (mir.track.TrajectoryFit attribute) n_loci (mir.cohort.LocusAlignment property) n_obs (mir.density.EnrichmentResult attribute) n_pairs (mir.bench.theory.CorrelationResult attribute) N_PROTOTYPES (in module mir.embedding.prototypes) n_prototypes (mir.embedding.presets.ChainPreset attribute) n_replicates (mir.repertoire.RarefyResult attribute) n_replicates() (in module mir.embedding.prototypes) n_samples (mir.explain.ChannelReport attribute) naive_reference() (in module mir.repertoire) names (mir.explain.ChannelSpec property) neighbor_enrichment() (in module mir.density) normalize_locus_alias() (in module mir.aliases) normalize_species_alias() (in module mir.aliases) O omega (mir.repertoire.RandomFourierFeatures attribute) P PairedTCREmp (class in mir.embedding.tcremp) pattern (mir.cohort.LocusAlignment property) pca (mir.density.DensitySpace attribute) pca_denoise() (in module mir.embedding.pca) pearson (mir.bench.theory.CorrelationResult attribute) perturb() (mir.twin.DonorTwin method) PgenRegressor (class in mir.ml.train) pick_device() (in module mir.ml.train) precision (mir.bench.metrics.AntigenMetric attribute) predict() (mir.ml.set_encoder.SetEncoderModel method) (mir.ml.train.PgenRegressor method) prototype_hash() (in module mir.ml.bundle) prototype_source_correlation() (in module mir.bench.theory) pvalue (mir.density.EnrichmentResult attribute) (mir.explain.ChannelReport attribute) pvalue_breadth (mir.density.EnrichmentResult attribute) pvalue_size (mir.density.EnrichmentResult attribute) Q qvalue (mir.density.EnrichmentResult attribute) R radius (mir.density.EnrichmentResult attribute) RandomFourierFeatures (class in mir.repertoire) rank (mir.explain.ChannelReport attribute) rao_gap() (mir.repertoire.RarefyResult method) rao_q() (in module mir.repertoire) rarefy_embedding() (in module mir.repertoire) RarefyResult (class in mir.repertoire) recall (mir.bench.metrics.AntigenMetric attribute) recovery_report() (in module mir.bench.eval) RepertoireDescriptor (class in mir.repertoire) RepertoireSpace (class in mir.repertoire) residualize() (in module mir.cohort) retention (mir.bench.metrics.AntigenMetric attribute) rff (mir.repertoire.RepertoireSpace attribute) rff2 (mir.repertoire.RepertoireSpace attribute) roundtrip() (mir.ml.codec.UnifiedCodec method) rows (mir.cohort.DonorCohort attribute) S s2_dissimilarity_distance_correlation() (in module mir.bench.theory) sample() (mir.generate.DescriptorDensity method) (mir.ml.diffusion.DiffusionModel method) sample_cloud() (mir.repertoire.RepertoireSpace method) sample_descriptor() (in module mir.repertoire) sample_embedding() (in module mir.repertoire) sample_statistics() (in module mir.repertoire) SampleEmbedding (class in mir.repertoire) save() (mir.cohort.DonorCohort method) (mir.ml.bundle.CodecBundle method) (mir.ml.diffusion.DiffusionModel method) (mir.ml.set_encoder.SetEncoderBundle method) (mir.repertoire.RepertoireSpace method) scalar (mir.repertoire.RepertoireDescriptor property) scaler (mir.density.DensitySpace attribute) score (mir.density.EnrichmentResult attribute) (mir.explain.ChannelReport attribute) second (mir.repertoire.SampleEmbedding attribute) seed_everything() (in module mir.ml.train) SequenceDecoder (class in mir.ml.decoder) SequenceEncoder (class in mir.ml.encoder) SetEncoder (class in mir.ml.set_encoder) SetEncoderBundle (class in mir.ml.set_encoder) SetEncoderModel (class in mir.ml.set_encoder) shm_embedding_drift() (in module mir.bench.theory) sigma2 (mir.repertoire.DepthThreshold attribute) (mir.track.TrajectoryFit attribute) simpson (mir.repertoire.RepertoireDescriptor attribute) simulate() (mir.twin.DonorTwin method) sizes (mir.repertoire.DepthThreshold attribute) space (mir.density.DensitySpace attribute) spaces (mir.cohort.DonorCohort attribute) spec (mir.cohort.DonorCohort attribute) (mir.explain.ChannelReport attribute) stack_embeddings() (in module mir.explain) strip_allele() (in module mir.alleles) T task (mir.ml.set_encoder.SetEncoderModel attribute) tau (mir.track.TrajectoryFit attribute) (mir.twin.DonorTwin attribute) tau2 (mir.repertoire.DepthThreshold attribute) TCREmp (class in mir.embedding.tcremp) tcrnet_convergence() (in module mir.bench.theory) tokens_to_seq() (in module mir.ml.decoder) top_interactions() (mir.track.TrajectoryFit method) train_diffusion() (in module mir.ml.diffusion) train_forward_encoder() (in module mir.ml.train) train_inverse_decoder() (in module mir.ml.train) train_pgen_regressor() (in module mir.ml.train) train_set_encoder() (in module mir.ml.set_encoder) train_unified_codec() (in module mir.ml.codec) TrajectoryFit (class in mir.track) transform (mir.ml.bundle.CodecBundle attribute) (mir.ml.set_encoder.SetEncoderBundle attribute) transform() (mir.cohort.DonorCohort method) (mir.density.DensitySpace method) (mir.repertoire.RandomFourierFeatures method) transform_clonotypes() (mir.repertoire.RepertoireSpace method) U UnifiedCodec (class in mir.ml.codec) V v_rep (mir.repertoire.RarefyResult attribute) vector (mir.repertoire.RepertoireDescriptor property) (mir.repertoire.SampleEmbedding property) W width (mir.explain.ChannelSpec property) X X (mir.cohort.DonorCohort attribute)