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.bulk.Deconvolution method) (omicverse.bulk.pyDEG method) (omicverse.bulk.pyGSEA method) (omicverse.bulk.pyPPI method) (omicverse.bulk.pyTCGA method) (omicverse.bulk.pyWGCNA method) (omicverse.bulk2single.Bulk2Single method) (omicverse.bulk2single.BulkTrajBlend method) (omicverse.bulk2single.Single2Spatial method) (omicverse.metabol.pyMetabo method) (omicverse.micro.Alpha method) (omicverse.micro.Beta method) (omicverse.micro.DA method) (omicverse.micro.MMvec method) (omicverse.micro.Ordinate method) (omicverse.pl.CellChatViz method) (omicverse.pl.ForbiddenCity method) (omicverse.pl.geneset_wordcloud method) (omicverse.single.Annotation method) (omicverse.single.AnnotationRef method) (omicverse.single.CellOntologyMapper method) (omicverse.single.CellVote method) (omicverse.single.cNMF method) (omicverse.single.DCT method) (omicverse.single.DEG method) (omicverse.single.Drug_Response method) (omicverse.single.Fate method) (omicverse.single.gene_trends method) (omicverse.single.GLUE_pair method) (omicverse.single.MetaCell method) (omicverse.single.MetaTiME method) (omicverse.single.Monocle method) (omicverse.single.pyCEFCON method) (omicverse.single.pyMOFA method) (omicverse.single.pyMOFAART method) (omicverse.single.pySCSA method) (omicverse.single.pySIMBA method) (omicverse.single.pyTOSICA method) (omicverse.single.pyVIA method) (omicverse.single.SCENIC method) (omicverse.single.TrajInfer method) (omicverse.single.Velo method) (omicverse.space.CellLoc method) (omicverse.space.CellMap method) (omicverse.space.Deconvolution method) (omicverse.space.GASTON method) (omicverse.space.pySpaceFlow method) (omicverse.space.pySTAGATE method) (omicverse.space.pySTAligner method) (omicverse.space.STT method) (omicverse.space.Tangram method) (omicverse.utils.LDA_topic method) A adata (omicverse.single.Monocle attribute) 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 (class in omicverse.micro) amplicon_16s_pipeline() (in module omicverse.alignment) ancombc() (omicverse.micro.DA method) 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 (class in omicverse.single) AnnotationRef (class in 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 (class in 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) braycurtis() (omicverse.micro.Beta method) build_amplicon_anndata() (in module omicverse.alignment) build_phylogeny() (in module omicverse.alignment) Bulk2Single (class in omicverse.bulk2single) bulk2single_plot_cellprop() (in module omicverse.bulk2single) bulk2single_plot_correlation() (in module omicverse.bulk2single) bulk_rnaseq_pipeline() (in module omicverse.alignment) BulkTrajBlend (class in 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 (class in omicverse.pl) CellLoc (class in omicverse.space) CellMap (class in omicverse.space) CellOntologyMapper (class in omicverse.single) cellproportion() (in module omicverse.pl) CellVote (class in 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 (class in omicverse.single) collapse_taxa() (in module omicverse.micro) combine_studies() (in module omicverse.micro) complexheatmap() (in module omicverse.pl) conditional_probabilities() (omicverse.micro.MMvec method) 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) cooccurrence() (omicverse.micro.MMvec method) 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 (class in omicverse.micro) dada2_pipeline() (in module omicverse.alignment) DCT (class in omicverse.single) Deconvolution (class in omicverse.bulk) (class in omicverse.space) decov_bulk_covid_bulk() (in module omicverse.datasets) decov_bulk_covid_single() (in module omicverse.datasets) DEG (class in omicverse.single) denoise() (in module omicverse.alignment.dada2) dentate_gyrus() (in module omicverse.datasets) dentate_gyrus_scvelo() (in module omicverse.datasets) dereplicate() (in module omicverse.alignment.vsearch) deseq2() (omicverse.micro.DA method) 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 (class in 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 (class in 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_and_trim() (in module omicverse.alignment.dada2) filter_by_prevalence() (in module omicverse.micro) filter_cells() (in module omicverse.pp) filter_genes() (in module omicverse.pp) filter_quality() (in module omicverse.alignment.vsearch) find_markers() (in module omicverse.single) fit() (omicverse.micro.MMvec method) ForbiddenCity (class in omicverse.pl) format_liana_results() (in module omicverse.single) fqdump() (in module omicverse.alignment) G GASTON (class in omicverse.space) gen_mpl_labels() (in module omicverse.pl) gene_trends (class in 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 (class in 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) (in module omicverse.single) 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 (class in omicverse.utils) learn_errors() (in module omicverse.alignment.dada2) 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) make_seqtab() (in module omicverse.alignment.dada2) 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) merge_pairs() (in module omicverse.alignment.dada2) meta_da() (in module omicverse.micro) MetaCell (class in omicverse.single) MetaTiME (class in omicverse.single) mixed_model() (in module omicverse.metabol) MMvec (class in omicverse.micro) module omicverse.external.GraphST moignard15() (in module omicverse.datasets) Monocle (class in 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) nmds() (omicverse.micro.Ordinate method) nmf_tissue_zones() (in module omicverse.space) normalize() (in module omicverse.metabol) normalize_pearson_residuals() (in module omicverse.pp) O observed() (omicverse.micro.Alpha method) omicverse.external.GraphST module opls_da() (in module omicverse.metabol) Ordinate (class in 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) pcoa() (omicverse.micro.Ordinate method) 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) proportion_explained() (omicverse.micro.Ordinate method) pyCEFCON (class in omicverse.single) pyDEG (class in omicverse.bulk) pyGSEA (class in omicverse.bulk) pyMetabo (class in omicverse.metabol) pyMOFA (class in omicverse.single) pyMOFAART (class in omicverse.single) pyPPI (class in omicverse.bulk) pySCSA (class in omicverse.single) pySIMBA (class in omicverse.single) pySpaceFlow (class in omicverse.space) pySTAGATE (class in omicverse.space) pySTAligner (class in omicverse.space) pyTCGA (class in omicverse.bulk) pyTOSICA (class in omicverse.single) pyVIA (class in omicverse.single) pyWGCNA (class in 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) remove_chimeras() (in module omicverse.alignment.dada2) 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() (omicverse.micro.Alpha method) 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 (class in 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) shannon() (omicverse.micro.Alpha method) significant_metabolites() (omicverse.metabol.pyMetabo method) simulate_paired() (in module omicverse.micro) Single2Spatial (class in omicverse.bulk2single) single_group_boxplot() (in module omicverse.pl) sintax() (in module omicverse.alignment.vsearch) 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 (class in 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 (class in omicverse.space) toggleswitch() (in module omicverse.datasets) top_pairs() (omicverse.micro.MMvec method) TrajInfer (class in omicverse.single) transform() (in module omicverse.metabol) tsne() (in module omicverse.pl) (in module omicverse.pp) U uchime3_denovo() (in module omicverse.alignment.vsearch) umap() (in module omicverse.pl) (in module omicverse.pp) unoise3() (in module omicverse.alignment.vsearch) update_classification_from_database() (in module omicverse.space) usearch_global() (in module omicverse.alignment.vsearch) V Velo (class in omicverse.single) venn() (in module omicverse.pl) violin() (in module omicverse.pl) vip_bar() (in module omicverse.metabol) vip_table() (omicverse.metabol.pyMetabo method) 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) wilcoxon() (omicverse.micro.DA method) wrap_dataframe() (in module omicverse.utils) write_visium_hd_cellseg() (in module omicverse.io.spatial) Z zebrafish() (in module omicverse.datasets)
