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) 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() (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) braycurtis() (omicverse.micro.Beta method) 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) 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() (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) 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() (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_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() (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) (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() (in module 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() (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) 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() (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) 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() (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) pyVIA() (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) 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() (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) shannon() (omicverse.micro.Alpha method) significant_metabolites() (omicverse.metabol.pyMetabo method) simulate_paired() (in module omicverse.micro) Single2Spatial() (in module 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() (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) top_pairs() (omicverse.micro.MMvec method) TrajInfer() (in module 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() (in module 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)
