Index _ | A | B | C | D | E | F | G | H | L | M | P | R | S | T | U | V _ __all__ (in module flashscenic) __repr__() (flashscenic.data.DownloadedResources method) (flashscenic.data.flashscenic.data.DownloadedResources.DownloadedResources method) _compute_auc() (in module flashscenic.aucell) _download_file() (in module flashscenic.data) _merge_regulons() (flashscenic.cistarget.CisTargetPruner method) (flashscenic.cistarget.flashscenic.cistarget.CisTargetPruner.CisTargetPruner method) _merge_regulons_by_tf() (flashscenic.cistarget.CisTargetPruner method) (flashscenic.cistarget.flashscenic.cistarget.CisTargetPruner.CisTargetPruner method) _register_scenic_resources() (in module flashscenic.data) _RESOURCE_REGISTRY (in module flashscenic.data) A AERTSLAB_BASE (in module flashscenic.data) ArrayLike (in module flashscenic.cistarget) (in module flashscenic.modules) B binarize() (in module flashscenic.modules), [1] C cache_dir (flashscenic.data.DownloadedResources attribute) (flashscenic.data.flashscenic.data.DownloadedResources.DownloadedResources attribute) category (flashscenic.data.ResourceFile attribute) CisTargetPruner (class in flashscenic.cistarget) clear_gpu_memory() (flashscenic.cistarget.CisTargetPruner method) (flashscenic.cistarget.flashscenic.cistarget.CisTargetPruner.CisTargetPruner method) compute_leading_edge() (in module flashscenic.cistarget) compute_nes() (in module flashscenic.cistarget), [1] compute_recovery_aucs() (in module flashscenic.cistarget), [1] D datasource (flashscenic.data.ResourceSet attribute) description (flashscenic.data.ResourceFile attribute) download_data() (in module flashscenic.data), [1] DownloadedResources (class in flashscenic.data) E expected_size_mb (flashscenic.data.ResourceFile attribute) F filename (flashscenic.data.ResourceFile attribute) files (flashscenic.data.ResourceSet attribute) filter_by_annotations() (in module flashscenic.cistarget), [1] filter_by_mapped_fraction() (in module flashscenic.modules), [1] filter_by_min_targets() (in module flashscenic.modules), [1] flashscenic module flashscenic.aucell module flashscenic.cistarget module flashscenic.cistarget.CisTargetPruner.CisTargetPruner (class in flashscenic.cistarget) flashscenic.cistarget.MotifAnnotation.MotifAnnotation (class in flashscenic.cistarget) flashscenic.data module flashscenic.data.DownloadedResources.DownloadedResources (class in flashscenic.data) flashscenic.modules module flashscenic.pipeline module flashscenic.rss module G genes_to_indices() (flashscenic.cistarget.CisTargetPruner method) (flashscenic.cistarget.flashscenic.cistarget.CisTargetPruner.CisTargetPruner method) get_annotation() (flashscenic.cistarget.flashscenic.cistarget.MotifAnnotation.MotifAnnotation method) (flashscenic.cistarget.MotifAnnotation method) get_aucell() (in module flashscenic.aucell), [1] get_enriched_motif_names() (flashscenic.cistarget.CisTargetPruner method) (flashscenic.cistarget.flashscenic.cistarget.CisTargetPruner.CisTargetPruner method) get_leading_edge_genes() (flashscenic.cistarget.CisTargetPruner method) (flashscenic.cistarget.flashscenic.cistarget.CisTargetPruner.CisTargetPruner method) get_target_indices() (in module flashscenic.modules), [1] GPUCisTargetPruner (in module flashscenic.cistarget) H has_annotation() (flashscenic.cistarget.flashscenic.cistarget.MotifAnnotation.MotifAnnotation method) (flashscenic.cistarget.MotifAnnotation method) L list_available_resources() (in module flashscenic.data), [1] load_annotations() (flashscenic.cistarget.CisTargetPruner method) (flashscenic.cistarget.flashscenic.cistarget.CisTargetPruner.CisTargetPruner method) load_database() (flashscenic.cistarget.CisTargetPruner method) (flashscenic.cistarget.flashscenic.cistarget.CisTargetPruner.CisTargetPruner method) load_from_file() (flashscenic.cistarget.flashscenic.cistarget.MotifAnnotation.MotifAnnotation class method) (flashscenic.cistarget.MotifAnnotation class method) load_from_tensor() (flashscenic.cistarget.CisTargetPruner method) (flashscenic.cistarget.flashscenic.cistarget.CisTargetPruner.CisTargetPruner method) M module flashscenic flashscenic.aucell flashscenic.cistarget flashscenic.data flashscenic.modules flashscenic.pipeline flashscenic.rss motif_annotation (flashscenic.data.DownloadedResources attribute) (flashscenic.data.flashscenic.data.DownloadedResources.DownloadedResources attribute) (flashscenic.data.ResourceSet property) MotifAnnotation (class in flashscenic.cistarget) MultiDatabaseCisTargetPruner (in module flashscenic.cistarget) P prune() (flashscenic.cistarget.CisTargetPruner method) (flashscenic.cistarget.flashscenic.cistarget.CisTargetPruner.CisTargetPruner method) prune_batch() (flashscenic.cistarget.CisTargetPruner method) (flashscenic.cistarget.flashscenic.cistarget.CisTargetPruner.CisTargetPruner method) prune_modules() (flashscenic.cistarget.CisTargetPruner method) (flashscenic.cistarget.flashscenic.cistarget.CisTargetPruner.CisTargetPruner method) prune_single_module() (in module flashscenic.cistarget), [1] R ranking_dbs (flashscenic.data.DownloadedResources attribute) (flashscenic.data.flashscenic.data.DownloadedResources.DownloadedResources attribute) (flashscenic.data.ResourceSet property) regulon_specificity_scores() (in module flashscenic.rss), [1] regulons_to_adjacency() (in module flashscenic), [1] ResourceFile (class in flashscenic.data) ResourceSet (class in flashscenic.data) run_flashscenic() (in module flashscenic.pipeline), [1] S select_knee_targets() (in module flashscenic.modules), [1] select_mixture_model_targets() (in module flashscenic.modules), [1] select_threshold_targets() (in module flashscenic.modules), [1] select_top_n_per_target() (in module flashscenic.modules), [1] select_topk_targets() (in module flashscenic.modules), [1] species (flashscenic.data.ResourceSet attribute) T tf_list (flashscenic.data.DownloadedResources attribute) (flashscenic.data.flashscenic.data.DownloadedResources.DownloadedResources attribute) (flashscenic.data.ResourceSet property) to_numpy() (in module flashscenic.modules), [1] U url (flashscenic.data.ResourceFile attribute) V version (flashscenic.data.ResourceSet attribute)