Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | V | Z _ __init__() (omicverse.fm.ModelRegistry method) (omicverse.fm.ModelSpec method) A Annotation() (in module omicverse.single) AnnotationRef() (in module omicverse.single) aucell() (in module omicverse.single) B bardotplot() (in module omicverse.pl) Batch() (in module omicverse.single) batch_correction() (in module omicverse.bulk) boxplot() (in module omicverse.pl) Bulk2Single() (in module omicverse.bulk2single) BulkTrajBlend() (in module omicverse.bulk2single) C Cal_Spatial_Net() (in module omicverse.space) CellChatViz() (in module omicverse.pl) CellOntologyMapper() (in module omicverse.single) cellphonedb_v5() (in module omicverse.single) cellproportion() (in module omicverse.pl) cellstackarea() (in module omicverse.pl) CellVote() (in module omicverse.single) clusters() (in module omicverse.space) cNMF() (in module omicverse.single) colormaps_palette() (in module omicverse.pl) cpdb_chord() (in module omicverse.pl) cpdb_heatmap() (in module omicverse.pl) cpdb_network() (in module omicverse.pl) create_mock_dataset() (in module omicverse.datasets) cytotrace2() (in module omicverse.single) D Deconvolution() (in module omicverse.bulk) (in module omicverse.space) DEG() (in module omicverse.single) dentate_gyrus() (in module omicverse.datasets) describe_model() (in module omicverse.fm) dotplot() (in module omicverse.pl) Drug_Response() (in module omicverse.single) E embedding() (in module omicverse.pl) embedding_atlas() (in module omicverse.pl) embedding_celltype() (in module omicverse.pl) embedding_density() (in module omicverse.pl) embedding_multi() (in module omicverse.pl) F Fate() (in module omicverse.single) filter_cells() (in module omicverse.pp) filter_genes() (in module omicverse.pp) ForbiddenCity() (in module omicverse.pl) G GASTON() (in module omicverse.space) geneset_aucell() (in module omicverse.single) geneset_enrichment() (in module omicverse.bulk) get_registry() (in module omicverse.fm) GLUE_pair() (in module omicverse.single) gptcelltype() (in module omicverse.single) gptcelltype_local() (in module omicverse.single) H highlight_spatial_region() (in module omicverse.pl) highly_variable_features() (in module omicverse.pp) highly_variable_genes() (in module omicverse.pp) I Integration() (in module omicverse.single) interpret_results() (in module omicverse.fm) L leiden() (in module omicverse.pp) list_models() (in module omicverse.fm) log1p() (in module omicverse.pp) louvain() (in module omicverse.pp) M marker_heatmap() (in module omicverse.pl) markers_dotplot() (in module omicverse.pl) Matrix_ID_mapping() (in module omicverse.bulk) mde() (in module omicverse.pp) MetaCell() (in module omicverse.single) MetaTiME() (in module omicverse.single) ModelRegistry (class in omicverse.fm) ModelSpec (class in omicverse.fm) moranI() (in module omicverse.space) N neighbors() (in module omicverse.pp) normalize_pearson_residuals() (in module omicverse.pp) normalize_total() (in module omicverse.pp) O optim_palette() (in module omicverse.pl) P palette_112 (in module omicverse.pl) palette_28 (in module omicverse.pl) pancreatic_endocrinogenesis() (in module omicverse.datasets) pbmc3k() (in module omicverse.datasets) pca() (in module omicverse.pl) (in module omicverse.pp) plot_boxplots() (in module omicverse.pl) plot_spatial() (in module omicverse.pl) predefined_signatures (in module omicverse.datasets) preprocess_validate() (in module omicverse.fm) profile_data() (in module omicverse.fm) pyDEG() (in module omicverse.bulk) pyGSEA() (in module omicverse.bulk) pyMOFA() (in module omicverse.single) pyMOFAART() (in module omicverse.single) pyPPI() (in module omicverse.bulk) pySCSA() (in module omicverse.single) pySIMBA() (in module omicverse.single) pySpaceFlow() (in module omicverse.space) pySTAGATE() (in module omicverse.space) pySTAligner() (in module omicverse.space) pyTCGA() (in module omicverse.bulk) pyTOSICA() (in module omicverse.single) Q qc() (in module omicverse.pp) R rank_genes_groups_dotplot() (in module omicverse.pl) read() (in module omicverse) read_10x_h5() (in module omicverse.io) read_10x_mtx() (in module omicverse.io) read_h5ad() (in module omicverse.io) read_nanostring() (in module omicverse.io) read_visium_hd() (in module omicverse.io) recover_counts() (in module omicverse.pp) regress() (in module omicverse.pp) regress_and_scale() (in module omicverse.pp) remove_cc_genes() (in module omicverse.pp) run() (in module omicverse.fm) S sc_color (in module omicverse.pl) scale() (in module omicverse.pp) SCENIC() (in module omicverse.single) score_genes_cell_cycle() (in module omicverse.pp) scrublet() (in module omicverse.pp) select_model() (in module omicverse.fm) Single2Spatial() (in module omicverse.bulk2single) spatial() (in module omicverse.pl) spatial_neighbors() (in module omicverse.space) STT() (in module omicverse.space) T Tangram() (in module omicverse.space) TrajInfer() (in module omicverse.single) tsne() (in module omicverse.pl) (in module omicverse.pp) U umap() (in module omicverse.pl) (in module omicverse.pp) V Velo() (in module omicverse.single) venn() (in module omicverse.pl) violin() (in module omicverse.pl) violin_box() (in module omicverse.pl) volcano() (in module omicverse.pl) Z zebrafish() (in module omicverse.datasets)