Index A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | Q | R | S | T | U | V | W | X | Z A acat_test() (in module cellink.at) add_module() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) add_vep_annos_to_gdata() (in module cellink.tl) aggregate() (cellink.DonorData method) aggregate_annotations_for_varm() (in module cellink.tl) all_gather() (cellink.ml.DonorMILModel method) apply() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) automatic_optimization (cellink.ml.DonorMILModel attribute) B backward() (cellink.ml.DonorMILModel method) bedgraph_to_snp_annotation() (in module cellink.tl.external) beta_weighting() (in module cellink.tl) bfloat16() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) buffers() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) C C (cellink.DonorData attribute), [1] calculate_ld() (in module cellink.tl.external) calculate_pcs() (in module cellink.tl.external) call_super_init (cellink.ml.DonorMILModel attribute) (cellink.tl.external.RegressionNLL attribute) (cellink.tl.external.SparseScore attribute) cell_level_obs_filter() (in module cellink.pp) cellink module cellink.at module cellink.io module cellink.ml module cellink.pl module cellink.pp module cellink.resources module cellink.tl module cellink.tl.external module cellink.utils module check_and_patch_ldsc_parse_bug() (in module cellink.tl.external) CHECKPOINT_HYPER_PARAMS_KEY (cellink.ml.DonorMILModel attribute) CHECKPOINT_HYPER_PARAMS_NAME (cellink.ml.DonorMILModel attribute) CHECKPOINT_HYPER_PARAMS_TYPE (cellink.ml.DonorMILModel attribute) children() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) clip_gradients() (cellink.ml.DonorMILModel method) column_normalize() (in module cellink.utils) combine_annotations() (in module cellink.tl) compile() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) compute_acat() (in module cellink.at) compute_celltype_programs() (in module cellink.tl.external) compute_diseaseprogression_programs() (in module cellink.tl.external) compute_escore() (in module cellink.tl.external) compute_joint_nmf_programs() (in module cellink.tl.external) compute_ld_scores_for_sclinker() (in module cellink.tl.external) compute_ld_scores_with_annotations_from_bimfile() (in module cellink.tl.external) compute_ld_scores_with_annotations_from_donor_data() (in module cellink.tl.external) compute_nmf_programs() (in module cellink.tl.external) configure_callbacks() (cellink.ml.DonorMILModel method) configure_gradient_clipping() (cellink.ml.DonorMILModel method) configure_ldsc_runner() (in module cellink.tl.external) configure_livi_runner() (in module cellink.tl.external) configure_model() (cellink.ml.DonorMILModel method) configure_optimizers() (cellink.ml.DonorMILModel method) configure_saigeqtl_runner() (in module cellink.tl.external) configure_sharded_model() (cellink.ml.DonorMILModel method) copy() (cellink.DonorData method) cpu() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) cuda() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) current_epoch (cellink.ml.DonorMILModel attribute) D device (cellink.ml.DonorMILModel attribute) device_mesh (cellink.ml.DonorMILModel attribute) donor_id (cellink.DonorData attribute) donor_level_obs_filter() (in module cellink.pp) donor_level_var_filter() (in module cellink.pp) DonorData (class in cellink) DonorMILModel (class in cellink.ml) dosage_per_strand() (in module cellink.utils) double() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) download_sclinker_enhancer_links() (in module cellink.tl.external) download_sclinker_references() (in module cellink.tl.external) dtype (cellink.ml.DonorMILModel attribute) dump_patches (cellink.ml.DonorMILModel attribute) (cellink.tl.external.RegressionNLL attribute) (cellink.tl.external.SparseScore attribute) E estimate_celltype_specific_heritability() (in module cellink.tl.external) estimate_genetic_correlation() (in module cellink.tl.external) estimate_heritability() (in module cellink.tl.external) estimate_ld_scores_from_bimfile() (in module cellink.tl.external) estimate_ld_scores_from_donor_data() (in module cellink.tl.external) eval() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) example_input_array (cellink.ml.DonorMILModel attribute) expression_by_genotype() (in module cellink.pl) extra_repr() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) F fabric (cellink.ml.DonorMILModel attribute) fit() (cellink.tl.external.JointNMFWrapper method) float() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) format_gsmap_sumstats() (in module cellink.tl.external) forward() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) freeze() (cellink.ml.DonorMILModel method) from_sgkit_dataset() (in module cellink.io) G G (cellink.DonorData attribute), [1] gaussianize() (in module cellink.utils) generate_gene_coord_file() (in module cellink.tl.external) generate_sldsc_genesets() (in module cellink.tl.external) genescores_to_100kb_bedgraph() (in module cellink.tl.external) genescores_to_abc_road_bedgraph() (in module cellink.tl.external) genescores_to_annotations() (in module cellink.tl.external) genesets_dir_to_entrez_gmt() (in module cellink.tl.external) get_1000genomes() (in module cellink.resources) get_1000genomes_frq() (in module cellink.resources) get_1000genomes_grch38() (in module cellink.resources) get_1000genomes_hapmap3() (in module cellink.resources) get_1000genomes_ld_scores() (in module cellink.resources) get_1000genomes_ld_weights() (in module cellink.resources) get_1000genomes_plink_files() (in module cellink.resources) get_association_testing_fn() (cellink.tl.external.LIVIRunner method) get_buffer() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) get_datamodule_classes() (cellink.tl.external.LIVIRunner method) get_disease_relevant_cells() (in module cellink.tl.external) get_dummy_onek1k() (in module cellink.resources) get_eqtl_catalog_dataset_associations() (in module cellink.resources) get_eqtl_catalog_datasets() (in module cellink.resources) get_extra_state() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) get_gwas_catalog_studies() (in module cellink.resources) get_gwas_catalog_study() (in module cellink.resources) get_gwas_catalog_study_summary_stats() (in module cellink.resources) get_livi_class() (cellink.tl.external.LIVIRunner method) get_livi_runner() (in module cellink.tl.external) get_magma_gene_loc() (in module cellink.tl.external) get_onek1k() (in module cellink.resources) get_parameter() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) get_pgs_catalog_score() (in module cellink.resources) get_pgs_catalog_scores() (in module cellink.resources) get_plink_commands_per_cell() (in module cellink.tl.external) get_saigeqtl_runner() (in module cellink.tl.external) get_snp_df() (in module cellink.tl) get_submodule() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) getBetaSNP() (cellink.at.GWAS method) getBetaSNPste() (cellink.at.GWAS method) getLRT() (cellink.at.GWAS method) getPv() (cellink.at.GWAS method) global_rank (cellink.ml.DonorMILModel attribute) global_step (cellink.ml.DonorMILModel attribute) GWAS (class in cellink.at) H half() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) Hd (cellink.tl.external.JointNMFWrapper attribute) Hh (cellink.tl.external.JointNMFWrapper attribute) hparams (cellink.ml.DonorMILModel attribute) hparams_initial (cellink.ml.DonorMILModel attribute) I infer_livi() (in module cellink.tl.external) ipu() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) J JointNMFWrapper (class in cellink.tl.external) L liftover_gwas_summary_stats() (in module cellink.resources) LIVIRunner (class in cellink.tl.external) load_abc_links() (in module cellink.tl.external) load_ensembl_to_entrez_map() (in module cellink.tl.external) load_from_checkpoint() (cellink.ml.DonorMILModel method) load_gene_annotation() (in module cellink.tl.external) load_gsmap_results() (in module cellink.tl.external) load_livi_results() (in module cellink.tl.external) load_roadmap_links() (in module cellink.tl.external) load_sclinker_heritability_results() (in module cellink.tl.external) load_state_dict() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) local_rank (cellink.ml.DonorMILModel attribute) locus() (in module cellink.pl) log() (cellink.ml.DonorMILModel method) log_dict() (cellink.ml.DonorMILModel method) log_transform() (in module cellink.pp) logger (cellink.ml.DonorMILModel attribute) loggers (cellink.ml.DonorMILModel attribute) low_abundance_filter() (in module cellink.pp) lr_scheduler_step() (cellink.ml.DonorMILModel method) lr_schedulers() (cellink.ml.DonorMILModel method) M make_annot_from_bimfile() (in module cellink.tl.external) make_annot_from_donor_data() (in module cellink.tl.external) make_group_file() (in module cellink.tl.external) manhattan() (in module cellink.pl) manual_backward() (cellink.ml.DonorMILModel method) merge_1000g_plink_chromosomes() (in module cellink.resources) mil_collate_fn() (in module cellink.ml) MILDataset (class in cellink.ml) missing_values_filter() (in module cellink.pp) module cellink cellink.at cellink.io cellink.ml cellink.pl cellink.pp cellink.resources cellink.tl cellink.tl.external cellink.utils modules() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) mtia() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) munge_sumstats() (in module cellink.tl.external) N named_buffers() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) named_children() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) named_modules() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) named_parameters() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) normalize() (in module cellink.pp) O on_after_backward() (cellink.ml.DonorMILModel method) on_after_batch_transfer() (cellink.ml.DonorMILModel method) on_before_backward() (cellink.ml.DonorMILModel method) on_before_batch_transfer() (cellink.ml.DonorMILModel method) on_before_optimizer_step() (cellink.ml.DonorMILModel method) on_before_zero_grad() (cellink.ml.DonorMILModel method) on_fit_end() (cellink.ml.DonorMILModel method) on_fit_start() (cellink.ml.DonorMILModel method) on_gpu (cellink.ml.DonorMILModel attribute) on_load_checkpoint() (cellink.ml.DonorMILModel method) on_predict_batch_end() (cellink.ml.DonorMILModel method) on_predict_batch_start() (cellink.ml.DonorMILModel method) on_predict_end() (cellink.ml.DonorMILModel method) on_predict_epoch_end() (cellink.ml.DonorMILModel method) on_predict_epoch_start() (cellink.ml.DonorMILModel method) on_predict_model_eval() (cellink.ml.DonorMILModel method) on_predict_start() (cellink.ml.DonorMILModel method) on_save_checkpoint() (cellink.ml.DonorMILModel method) on_test_batch_end() (cellink.ml.DonorMILModel method) on_test_batch_start() (cellink.ml.DonorMILModel method) on_test_end() (cellink.ml.DonorMILModel method) on_test_epoch_end() (cellink.ml.DonorMILModel method) on_test_epoch_start() (cellink.ml.DonorMILModel method) on_test_model_eval() (cellink.ml.DonorMILModel method) on_test_model_train() (cellink.ml.DonorMILModel method) on_test_start() (cellink.ml.DonorMILModel method) on_train_batch_end() (cellink.ml.DonorMILModel method) on_train_batch_start() (cellink.ml.DonorMILModel method) on_train_end() (cellink.ml.DonorMILModel method) on_train_epoch_end() (cellink.ml.DonorMILModel method) on_train_epoch_start() (cellink.ml.DonorMILModel method) on_train_start() (cellink.ml.DonorMILModel method) on_validation_batch_end() (cellink.ml.DonorMILModel method) on_validation_batch_start() (cellink.ml.DonorMILModel method) on_validation_end() (cellink.ml.DonorMILModel method) on_validation_epoch_end() (cellink.ml.DonorMILModel method) on_validation_epoch_start() (cellink.ml.DonorMILModel method) on_validation_model_eval() (cellink.ml.DonorMILModel method) on_validation_model_train() (cellink.ml.DonorMILModel method) on_validation_model_zero_grad() (cellink.ml.DonorMILModel method) on_validation_start() (cellink.ml.DonorMILModel method) one_hot_encode_genotypes() (in module cellink.utils) optimizer_step() (cellink.ml.DonorMILModel method) optimizer_zero_grad() (cellink.ml.DonorMILModel method) optimizers() (cellink.ml.DonorMILModel method) P parameters() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) predict_dataloader() (cellink.ml.DonorMILModel method) predict_step() (cellink.ml.DonorMILModel method) prep_repr() (cellink.DonorData method) prepare_data() (cellink.ml.DonorMILModel method) prepare_scprs_data() (in module cellink.tl.external) preprocess_for_sldsc() (in module cellink.tl.external) print() (cellink.ml.DonorMILModel method) Q qq() (in module cellink.pl) R read_bgen() (in module cellink.io) read_dd() (in module cellink.io) read_h5_dd() (in module cellink.io) read_jaxqtl_results() (in module cellink.tl.external) read_pgen_zarr() (in module cellink.io) read_plink() (in module cellink.io) read_saigeqtl_results() (in module cellink.tl.external) read_sgkit_zarr() (in module cellink.io) read_tensorqtl_results() (in module cellink.tl.external) read_zarr_dd() (in module cellink.io) register_backward_hook() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) register_buffer() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) register_forward_hook() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) register_forward_pre_hook() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) register_full_backward_hook() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) register_full_backward_pre_hook() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) register_load_state_dict_post_hook() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) register_load_state_dict_pre_hook() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) register_module() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) register_parameter() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) register_state_dict_post_hook() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) register_state_dict_pre_hook() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) RegressionNLL (class in cellink.tl.external) remove_ignored_hparams() (cellink.ml.DonorMILModel method) requires_grad_() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) resolve_device() (cellink.tl.external.LIVIRunner method) run_burden_test() (in module cellink.tl) run_favor() (in module cellink.tl) run_jaxqtl() (in module cellink.tl.external) run_livi_association_testing() (in module cellink.tl.external) run_magma_annotate() (in module cellink.tl.external) run_magma_gene_analysis() (in module cellink.tl.external) run_magma_gpa() (in module cellink.tl.external) run_magma_gsa() (in module cellink.tl.external) run_magma_pipeline() (in module cellink.tl.external) run_mixmil() (in module cellink.tl.external) run_saigeqtl() (in module cellink.tl.external) run_scdrs() (in module cellink.tl.external) run_sclinker_heritability() (in module cellink.tl.external) run_scprs_pipeline() (in module cellink.tl.external) run_seismic() (in module cellink.tl.external) run_seismic_torch() (in module cellink.tl.external) run_skat_test() (in module cellink.tl) run_snpeff() (in module cellink.tl) run_tensorqtl() (in module cellink.tl.external) run_test() (cellink.at.Skat method) run_vep() (in module cellink.tl) S save_hyperparameters() (cellink.ml.DonorMILModel method) save_livi_results() (in module cellink.tl.external) scores_to_covar() (in module cellink.tl.external) scores_to_gmt() (in module cellink.tl.external) sel() (cellink.DonorData method) set_extra_state() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) set_submodule() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) setup() (cellink.ml.DonorMILModel method) shape (cellink.DonorData attribute) share_memory() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) Skat (class in cellink.at) SparseScore (class in cellink.tl.external) state_dict() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) stream_pgen_to_zarr() (in module cellink.io) strict_loading (cellink.ml.DonorMILModel attribute) subset_gene() (in module cellink.tl) subset_genomic_region() (in module cellink.tl) T T_destination (cellink.ml.DonorMILModel attribute) (cellink.tl.external.RegressionNLL attribute) (cellink.tl.external.SparseScore attribute) teardown() (cellink.ml.DonorMILModel method) test_association() (cellink.at.GWAS method) test_dataloader() (cellink.ml.DonorMILModel method) test_step() (cellink.ml.DonorMILModel method) to() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) to_empty() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) to_onnx() (cellink.ml.DonorMILModel method) to_plink() (in module cellink.io) to_tensorrt() (cellink.ml.DonorMILModel method) to_torchscript() (cellink.ml.DonorMILModel method) toggle_optimizer() (cellink.ml.DonorMILModel method) toggled_optimizer() (cellink.ml.DonorMILModel method) train() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) train_dataloader() (cellink.ml.DonorMILModel method) train_livi() (in module cellink.tl.external) trainer (cellink.ml.DonorMILModel attribute) training (cellink.ml.DonorMILModel attribute) (cellink.tl.external.RegressionNLL attribute) (cellink.tl.external.SparseScore attribute) training_step() (cellink.ml.DonorMILModel method) transfer_batch_to_device() (cellink.ml.DonorMILModel method) type() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) U unfreeze() (cellink.ml.DonorMILModel method) untoggle_optimizer() (cellink.ml.DonorMILModel method) V val_dataloader() (cellink.ml.DonorMILModel method) validation_step() (cellink.ml.DonorMILModel method) variant_qc() (in module cellink.pp) volcano() (in module cellink.pl) W Wd (cellink.tl.external.JointNMFWrapper attribute) Wh (cellink.tl.external.JointNMFWrapper attribute) write_dd() (cellink.DonorData method) write_h5_dd() (cellink.DonorData method) write_slurm_array_job() (in module cellink.tl.external) write_variants_to_vcf() (in module cellink.io) write_zarr_dd() (cellink.DonorData method) X xpu() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method) Z zero_grad() (cellink.ml.DonorMILModel method) (cellink.tl.external.RegressionNLL method) (cellink.tl.external.SparseScore method)