Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z _ __init__() (omicverse.pl.geneset_wordcloud method) A adata (in module omicverse.single) add_density_contour() (in module omicverse.pl) add_palue() (in module omicverse.pl) add_pie2spatial() (in module omicverse.pl) add_streamplot() (in module omicverse.pl) aggregate_by_class() (in module omicverse.metabol) Alpha() (in module omicverse.micro) amplicon_16s_pipeline() (in module omicverse.alignment) anndata_to_CPU() (in module omicverse.pp) anndata_to_GPU() (in module omicverse.pp) annotate_lipids() (in module omicverse.metabol) annotate_peaks() (in module omicverse.metabol) Annotation() (in module omicverse.single) AnnotationRef() (in module omicverse.single) anova() (in module omicverse.metabol) asca() (in module omicverse.metabol) asca_variance_bar() (in module omicverse.metabol) attach_tree() (in module omicverse.micro) auto_resolution() (in module omicverse.single) autoResolution() (in module omicverse.single) B bardotplot() (in module omicverse.pl) batch_correction() (in module omicverse.bulk) (in module omicverse.single) Beta() (in module omicverse.micro) bhattacherjee() (in module omicverse.datasets) bin2cell() (in module omicverse.space) binary_search() (in module omicverse.pp) biomarker_panel() (in module omicverse.metabol) blank_filter() (in module omicverse.metabol) blobs() (in module omicverse.datasets) bm() (in module omicverse.datasets) bone_marrow() (in module omicverse.datasets) boxplot() (in module omicverse.pl) branch_streamplot() (in module omicverse.pl) build_amplicon_anndata() (in module omicverse.alignment) build_phylogeny() (in module omicverse.alignment) Bulk2Single() (in module omicverse.bulk2single) bulk2single_plot_cellprop() (in module omicverse.bulk2single) bulk2single_plot_correlation() (in module omicverse.bulk2single) bulk_rnaseq_pipeline() (in module omicverse.alignment) BulkTrajBlend() (in module omicverse.bulk2single) burczynski06() (in module omicverse.datasets) C cal_paga() (in module omicverse.utils) Cal_Spatial_Net() (in module omicverse.space) calculate_gene_density() (in module omicverse.pl) calculate_gene_signature() (in module omicverse.space) call_tool() (in module omicverse.utils.biocontext) CAST() (in module omicverse.space) ccc_heatmap() (in module omicverse.pl) ccc_network_plot() (in module omicverse.pl) ccc_stat_plot() (in module omicverse.pl) cell_cor_heatmap() (in module omicverse.pl) cellcharter() (in module omicverse.space) CellChatViz() (in module omicverse.pl) CellLoc() (in module omicverse.space) CellMap() (in module omicverse.space) CellOntologyMapper() (in module omicverse.single) cellproportion() (in module omicverse.pl) CellVote() (in module omicverse.single) champ() (in module omicverse.pp) chromaffin() (in module omicverse.datasets) cite_seq() (in module omicverse.datasets) clr() (in module omicverse.micro) cluster() (in module omicverse.utils) clusters() (in module omicverse.space) cNMF() (in module omicverse.single) collapse_taxa() (in module omicverse.micro) combine_studies() (in module omicverse.micro) complexheatmap() (in module omicverse.pl) contour() (in module omicverse.pl) convert2gene_id() (in module omicverse.utils) convert2gene_symbol() (in module omicverse.utils) convert2symbol() (in module omicverse.utils) convert_adata_for_rust() (in module omicverse.utils) convert_human_to_mouse_network() (in module omicverse.single) convert_to_pandas() (in module omicverse.utils) ConvexHull() (in module omicverse.pl) corr_network() (in module omicverse.metabol) corr_network_plot() (in module omicverse.metabol) cosg() (in module omicverse.single) count() (in module omicverse.alignment) cpu_gpu_mixed_init() (omicverse.settings method) create_communication_anndata() (in module omicverse.space) create_custom_colormap() (in module omicverse.pl) create_mock_dataset() (in module omicverse.datasets) crop_space_visium() (in module omicverse.space) cutadapt() (in module omicverse.alignment) cv_filter() (in module omicverse.metabol) cytotrace2() (in module omicverse.single) D DA() (in module omicverse.micro) dada2_pipeline() (in module omicverse.alignment) DCT() (in module omicverse.single) Deconvolution() (in module omicverse.bulk) (in module omicverse.space) decov_bulk_covid_bulk() (in module omicverse.datasets) decov_bulk_covid_single() (in module omicverse.datasets) DEG() (in module omicverse.single) dentate_gyrus() (in module omicverse.datasets) dentate_gyrus_scvelo() (in module omicverse.datasets) dgca() (in module omicverse.metabol) dgca_class_bar() (in module omicverse.metabol) differential() (in module omicverse.metabol) dotplot() (in module omicverse.pl) download_CaDRReS_model() (in module omicverse.utils) download_cellphonedb_database() (in module omicverse.single) download_cl() (in module omicverse.single) download_data() (in module omicverse.datasets) download_data_requests() (in module omicverse.datasets) download_GDSC_data() (in module omicverse.utils) download_geneid_annotation_pair() (in module omicverse.utils) download_pathway_database() (in module omicverse.utils) download_tosica_gmt() (in module omicverse.utils) drift_correct() (in module omicverse.metabol) Drug_Response() (in module omicverse.single) dynamic_features() (in module omicverse.single) dynamic_heatmap() (in module omicverse.pl) dynamic_trends() (in module omicverse.pl) E embedding() (in module omicverse.pl) embedding_adjust() (in module omicverse.pl) embedding_atlas() (in module omicverse.pl) embedding_celltype() (in module omicverse.pl) embedding_density() (in module omicverse.pl) F factor_correlation() (in module omicverse.single) factor_exact() (in module omicverse.single) fastp() (in module omicverse.alignment) fasttree() (in module omicverse.alignment) Fate() (in module omicverse.single) feature_heatmap() (in module omicverse.pl) featureCount() (in module omicverse.alignment) fetch_chebi_compounds() (in module omicverse.metabol) fetch_franzosa_ibd_2019() (in module omicverse.micro) fetch_hmdb_from_name() (in module omicverse.metabol) fetch_kegg_pathways() (in module omicverse.metabol) fetch_lion_associations() (in module omicverse.metabol) fetch_rdp() (in module omicverse.alignment) fetch_silva() (in module omicverse.alignment) fetch_sintax_ref() (in module omicverse.alignment) filter_by_prevalence() (in module omicverse.micro) filter_cells() (in module omicverse.pp) filter_genes() (in module omicverse.pp) find_markers() (in module omicverse.single) ForbiddenCity() (in module omicverse.pl) format_liana_results() (in module omicverse.single) fqdump() (in module omicverse.alignment) G GASTON() (in module omicverse.space) gen_mpl_labels() (in module omicverse.pl) gene_trends() (in module omicverse.single) generate_reference_table() (in module omicverse) generate_scRNA_report() (in module omicverse.single) geneset_aucell() (in module omicverse.single) geneset_enrichment() (in module omicverse.bulk) geneset_plot() (in module omicverse.bulk) geneset_plot_multi() (in module omicverse.bulk) geneset_prepare() (in module omicverse.utils) geneset_wordcloud (class in omicverse.pl) get_adata() (in module omicverse.datasets) get_celltype_marker() (in module omicverse.single) get_cluster_celltype() (in module omicverse.single) get_ensembl_id() (in module omicverse.utils.biocontext) get_fulltext() (in module omicverse.utils.biocontext) get_gene_annotation() (in module omicverse.utils) get_markers() (in module omicverse.single) get_obs_value() (in module omicverse.single) get_uniprot_id() (in module omicverse.utils.biocontext) get_weights() (in module omicverse.single) gillespie() (in module omicverse.datasets) GLUE_pair() (in module omicverse.single) gptcelltype() (in module omicverse.single) gptcelltype_local() (in module omicverse.single) gpu_init() (omicverse.settings method) group_heatmap() (in module omicverse.pl) gtf_to_pair_tsv() (in module omicverse.utils) H haber() (in module omicverse.datasets) hematopoiesis() (in module omicverse.datasets) hematopoiesis_raw() (in module omicverse.datasets) hg_forebrain_glutamatergic() (in module omicverse.datasets) highly_variable_features() (in module omicverse.pp) highly_variable_genes() (in module omicverse.pp) hl60() (in module omicverse.datasets) human_tfs() (in module omicverse.datasets) I identify_robust_genes() (in module omicverse.pp) ilr() (in module omicverse.micro) impute() (in module omicverse.metabol) K krumsiek11() (in module omicverse.datasets) L lazy() (in module omicverse.single) LDA_topic() (in module omicverse.utils) leiden() (in module omicverse.pp) lion_enrichment() (in module omicverse.metabol) list_tools() (in module omicverse.utils.biocontext) load() (in module omicverse.io) load_human_prior_interaction_network() (in module omicverse.single) load_metabolights() (in module omicverse.utils) load_pathways() (in module omicverse.metabol) log1p() (in module omicverse.pp) louvain() (in module omicverse.pp) M mafft() (in module omicverse.alignment) map_ids() (in module omicverse.metabol) map_spatial_auto() (in module omicverse.space) map_spatial_manual() (in module omicverse.space) marker_heatmap() (in module omicverse.pl) markers_dotplot() (in module omicverse.pl) Matrix_ID_mapping() (in module omicverse.bulk) mde() (in module omicverse.pp) (in module omicverse.utils) meba() (in module omicverse.metabol) merge_cluster() (in module omicverse.space) meta_da() (in module omicverse.micro) MetaCell() (in module omicverse.single) MetaTiME() (in module omicverse.single) mixed_model() (in module omicverse.metabol) MMvec() (in module omicverse.micro) module omicverse.external.GraphST moignard15() (in module omicverse.datasets) Monocle() (in module omicverse.single) moranI() (in module omicverse.space) mouse_hsc_nestorowa16() (in module omicverse.single) msea_gsea() (in module omicverse.metabol) msea_ora() (in module omicverse.metabol) multi_brain_5k() (in module omicverse.datasets) mummichog_basic() (in module omicverse.metabol) N nascseq() (in module omicverse.datasets) neighbors() (in module omicverse.pp) nmf_tissue_zones() (in module omicverse.space) normalize() (in module omicverse.metabol) normalize_pearson_residuals() (in module omicverse.pp) O omicverse.external.GraphST module opls_da() (in module omicverse.metabol) Ordinate() (in module omicverse.micro) P paired_cca() (in module omicverse.micro) paired_spearman() (in module omicverse.micro) palette() (in module omicverse.pl) pancreas_cellrank() (in module omicverse.datasets) pancreatic_endocrinogenesis() (in module omicverse.datasets) parallel_fastq_dump() (in module omicverse.alignment) parse_lipid() (in module omicverse.metabol) pathway_aucell() (in module omicverse.single) pathway_aucell_enrichment() (in module omicverse.single) pathway_bar() (in module omicverse.metabol) pathway_dot() (in module omicverse.metabol) pathway_enrichment() (in module omicverse.single) pathway_enrichment_plot() (in module omicverse.single) paul15() (in module omicverse.datasets) pbmc3k() (in module omicverse.datasets) pbmc8k() (in module omicverse.datasets) pca() (in module omicverse.pp) plot1cell() (in module omicverse.pl) plot_cellproportion() (in module omicverse.pl) plot_embedding_biplot() (in module omicverse.micro) plot_embedding_celltype() (in module omicverse.pl) plot_flowsig_network() (in module omicverse.pl) plot_grouped_fractions() (in module omicverse.pl) plot_metacells() (in module omicverse.single) plot_mmvec_training() (in module omicverse.micro) plot_paga() (in module omicverse.utils) plot_pca_variance_ratio() (in module omicverse.pl) plot_set() (in module omicverse.pl) plot_spatial() (in module omicverse.pl) plot_text_set() (in module omicverse.pl) plsda() (in module omicverse.metabol) prefetch() (in module omicverse.alignment) preprocess() (in module omicverse.pp) pyCEFCON() (in module omicverse.single) pyDEG() (in module omicverse.bulk) pyGSEA() (in module omicverse.bulk) pyMetabo() (in module omicverse.metabol) 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) pyWGCNA() (in module omicverse.bulk) Q qc() (in module omicverse.pp) query_alphafold() (in module omicverse.utils.biocontext) query_cell_ontology() (in module omicverse.utils.biocontext) query_chebi() (in module omicverse.utils.biocontext) query_efo() (in module omicverse.utils.biocontext) query_go() (in module omicverse.utils.biocontext) query_hpa() (in module omicverse.utils.biocontext) query_interpro() (in module omicverse.utils.biocontext) query_opentargets() (in module omicverse.utils.biocontext) query_panglaodb() (in module omicverse.utils.biocontext) query_reactome() (in module omicverse.utils.biocontext) query_string() (in module omicverse.utils.biocontext) query_uniprot() (in module omicverse.utils.biocontext) R rank_genes_groups_dotplot() (in module omicverse.pl) rarefy() (in module omicverse.micro) read() (in module omicverse.io) read_10x_h5() (in module omicverse.io) read_10x_mtx() (in module omicverse.io) read_csv() (in module omicverse.io) read_h5ad() (in module omicverse.io) read_lcms() (in module omicverse.metabol) read_metaboanalyst() (in module omicverse.metabol) read_nanostring() (in module omicverse.io) read_visium() (in module omicverse.io.spatial) read_visium_10x() (in module omicverse.space) read_visium_hd() (in module omicverse.io) read_visium_hd_bin() (in module omicverse.io) read_visium_hd_seg() (in module omicverse.io) read_wide() (in module omicverse.metabol) read_xenium() (in module omicverse.io) readWGCNA() (in module omicverse.bulk) recover_counts() (in module omicverse.pp) ref() (in module omicverse.alignment) refine_label() (in module omicverse.utils) regress() (in module omicverse.pp) regress_and_scale() (in module omicverse.pp) remove_cc_genes() (in module omicverse.pp) retrieve_layers() (in module omicverse.utils) roc_feature() (in module omicverse.metabol) roe() (in module omicverse.utils) rotate_space_visium() (in module omicverse.space) run_cellphonedb_v5() (in module omicverse.single) run_liana() (in module omicverse.single) run_mofa() (in module omicverse.metabol) S s_plot() (in module omicverse.metabol) salvage_secondary_labels() (in module omicverse.space) sample_qc() (in module omicverse.metabol) sample_qc_plot() (in module omicverse.metabol) save() (in module omicverse.io) sc_ref_Lymph_Node() (in module omicverse.datasets) scale() (in module omicverse.pp) scanpy_cellanno_from_dict() (in module omicverse.single) SCENIC() (in module omicverse.single) sceu_seq_organoid() (in module omicverse.datasets) sceu_seq_rpe1() (in module omicverse.datasets) scifate() (in module omicverse.datasets) scnt_seq_neuron_labeling() (in module omicverse.datasets) scnt_seq_neuron_splicing() (in module omicverse.datasets) score_genes_cell_cycle() (in module omicverse.pp) scrublet() (in module omicverse.pp) scrublet_simulate_doublets() (in module omicverse.pp) scslamseq() (in module omicverse.datasets) search_clinical_trials() (in module omicverse.utils.biocontext) search_drugs() (in module omicverse.utils.biocontext) search_interpro() (in module omicverse.utils.biocontext) search_literature() (in module omicverse.utils.biocontext) search_preprints() (in module omicverse.utils.biocontext) search_pride() (in module omicverse.utils.biocontext) select_hvf_pegasus() (in module omicverse.pp) seqfish() (in module omicverse.datasets) serrf() (in module omicverse.metabol) simulate_paired() (in module omicverse.micro) Single2Spatial() (in module omicverse.bulk2single) single_group_boxplot() (in module omicverse.pl) spatial_autocorr() (in module omicverse.space) spatial_neighbors() (in module omicverse.space) STAR() (in module omicverse.alignment) store_layers() (in module omicverse.utils) string_interaction() (in module omicverse.bulk) STT() (in module omicverse.space) sude() (in module omicverse.pp) svg() (in module omicverse.space) symbol2id() (in module omicverse.utils) sync_visium_hd_seg_geometries() (in module omicverse.space) T Tangram() (in module omicverse.space) toggleswitch() (in module omicverse.datasets) TrajInfer() (in module omicverse.single) transform() (in module omicverse.metabol) tsne() (in module omicverse.pl) (in module omicverse.pp) U umap() (in module omicverse.pl) (in module omicverse.pp) update_classification_from_database() (in module omicverse.space) V Velo() (in module omicverse.single) venn() (in module omicverse.pl) violin() (in module omicverse.pl) vip_bar() (in module omicverse.metabol) visium_10x_hd_cellpose_expand() (in module omicverse.space) visium_10x_hd_cellpose_gex() (in module omicverse.space) visium_10x_hd_cellpose_he() (in module omicverse.space) volcano() (in module omicverse.metabol) (in module omicverse.pl) W weighted_knn_trainer() (in module omicverse.utils) weighted_knn_transfer() (in module omicverse.utils) wrap_dataframe() (in module omicverse.utils) Z zebrafish() (in module omicverse.datasets)
