Index A | C | D | G | M | N | P | R | S | W A add_latent() (in module scripts.metasigs.early_integration.get_signatures) AvgBulkScorer (class in scripts.metrics.corrs) (class in scripts.metrics.score_bulk) C corr_signatures() (in module scripts.metrics.corrs) D determine_seq_technology() (in module scripts.preprocessing.preprocessing) G get_adata() (in module scripts.metrics.corrs) get_all_scores() (in module scripts.metrics.corrs) (in module scripts.metrics.score_bulk) get_args() (in module scripts.metasigs.early_integration.bbknn_latent) (in module scripts.metasigs.early_integration.get_signatures) (in module scripts.metasigs.early_integration.harmony_latent) (in module scripts.metasigs.early_integration.scvi_latent) (in module scripts.metasigs.early_integration.unintegrated) (in module scripts.metrics.aggregate_methods) (in module scripts.metrics.aggregate_signatures) (in module scripts.metrics.corrs) (in module scripts.metrics.eval) (in module scripts.metrics.eval_overlap) (in module scripts.metrics.marker_overlap) (in module scripts.metrics.score_bulk) (in module scripts.preprocessing.preprocessing) (in module scripts.preprocessing.subsample) get_cluster() (in module scripts.metasigs.early_integration.get_signatures) get_counts_from_tpm() (in module scripts.preprocessing.preprocessing) get_counts_per_cell() (in module scripts.preprocessing.preprocessing) get_data() (in module scripts.metrics.score_bulk) get_latent() (in module scripts.metasigs.early_integration.bbknn_latent) (in module scripts.metasigs.early_integration.harmony_latent) (in module scripts.metasigs.early_integration.scvi_latent) get_metasigs() (in module scripts.metasigs.early_integration.get_signatures) get_overlap() (in module scripts.metrics.marker_overlap) get_score() (in module scripts.metrics.eval) (in module scripts.metrics.eval_overlap) get_scores() (in module scripts.metrics.corrs) get_tpm_counts() (in module scripts.preprocessing.preprocessing) M main() (in module scripts.metasigs.early_integration.bbknn_latent) (in module scripts.metasigs.early_integration.get_signatures) (in module scripts.metasigs.early_integration.harmony_latent) (in module scripts.metasigs.early_integration.scvi_latent) (in module scripts.metasigs.early_integration.unintegrated) (in module scripts.metrics.aggregate_methods) (in module scripts.metrics.aggregate_signatures) (in module scripts.metrics.corrs) (in module scripts.metrics.eval) (in module scripts.metrics.eval_overlap) (in module scripts.metrics.marker_overlap) (in module scripts.metrics.score_bulk) (in module scripts.preprocessing.preprocessing) (in module scripts.preprocessing.subsample) make_datadir() (in module scripts.preprocessing.preprocessing) module scripts.metasigs.early_integration.bbknn_latent scripts.metasigs.early_integration.get_signatures scripts.metasigs.early_integration.harmony_latent scripts.metasigs.early_integration.scvi_latent scripts.metasigs.early_integration.unintegrated scripts.metrics.aggregate_methods scripts.metrics.aggregate_signatures scripts.metrics.corrs scripts.metrics.eval scripts.metrics.eval_overlap scripts.metrics.marker_overlap scripts.metrics.score_bulk scripts.preprocessing.preprocessing scripts.preprocessing.subsample N normalize() (in module scripts.preprocessing.preprocessing) P preprocessing() (in module scripts.preprocessing.preprocessing) R r_names() (in module scripts.preprocessing.preprocessing) read_anndata() (in module scripts.metasigs.early_integration.bbknn_latent) (in module scripts.metasigs.early_integration.get_signatures) (in module scripts.metasigs.early_integration.harmony_latent) (in module scripts.metasigs.early_integration.scvi_latent) (in module scripts.metasigs.early_integration.unintegrated) (in module scripts.preprocessing.preprocessing) remove_excluded_samples() (in module scripts.preprocessing.preprocessing) remove_high_mt_cells() (in module scripts.preprocessing.preprocessing) remove_low_count_cells() (in module scripts.preprocessing.preprocessing) remove_samples() (in module scripts.preprocessing.preprocessing) S score() (scripts.metrics.corrs.AvgBulkScorer method) (scripts.metrics.score_bulk.AvgBulkScorer method) score_cell_cycle() (in module scripts.preprocessing.preprocessing) score_dataset() (in module scripts.metrics.corrs) (in module scripts.metrics.score_bulk) score_signature() (in module scripts.metrics.corrs) scripts.metasigs.early_integration.bbknn_latent module scripts.metasigs.early_integration.get_signatures module scripts.metasigs.early_integration.harmony_latent module scripts.metasigs.early_integration.scvi_latent module scripts.metasigs.early_integration.unintegrated module scripts.metrics.aggregate_methods module scripts.metrics.aggregate_signatures module scripts.metrics.corrs module scripts.metrics.eval module scripts.metrics.eval_overlap module scripts.metrics.marker_overlap module scripts.metrics.score_bulk module scripts.preprocessing.preprocessing module scripts.preprocessing.subsample module set_tpm_counts() (in module scripts.preprocessing.preprocessing) subset_malignant() (in module scripts.preprocessing.preprocessing) W write_anndata() (in module scripts.preprocessing.preprocessing)
