# User API Import OmicVerse as: ```python import omicverse as ov ``` This page is auto-generated from `@register_function` entries in the OmicVerse registry. Public registry entries listed here: 414 ```{eval-rst} .. currentmodule:: omicverse ``` ## Top-Level API ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: generate_reference_table ``` ## Settings ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: settings.cpu_gpu_mixed_init settings.gpu_init ``` ## Data IO ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: io.load io.read io.read_10x_h5 io.read_10x_mtx io.read_csv io.read_h5ad io.read_nanostring io.read_visium_hd io.read_visium_hd_bin io.read_visium_hd_seg io.read_xenium io.save io.spatial.read_visium io.write_visium_hd_cellseg ``` ## Alignment ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: alignment.amplicon_16s_pipeline alignment.build_amplicon_anndata alignment.build_phylogeny alignment.bulk_rnaseq_pipeline alignment.count alignment.cutadapt alignment.dada2_pipeline alignment.denoise alignment.dereplicate alignment.fastp alignment.fasttree alignment.featureCount alignment.fetch_rdp alignment.fetch_silva alignment.fetch_sintax_ref alignment.filter_and_trim alignment.filter_quality alignment.fqdump alignment.learn_errors alignment.mafft alignment.make_seqtab alignment.merge_pairs alignment.parallel_fastq_dump alignment.prefetch alignment.ref alignment.remove_chimeras alignment.sintax alignment.STAR alignment.uchime3_denovo alignment.unoise3 alignment.usearch_global ``` ## Preprocessing (`pp`) ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pp.anndata_to_CPU pp.anndata_to_GPU pp.binary_search pp.champ pp.filter_cells pp.filter_genes pp.highly_variable_features pp.highly_variable_genes pp.identify_robust_genes pp.leiden pp.log1p pp.louvain pp.mde pp.neighbors pp.normalize_pearson_residuals pp.pca pp.preprocess pp.qc pp.recover_counts pp.regress pp.regress_and_scale pp.remove_cc_genes pp.scale pp.score_genes_cell_cycle pp.scrublet pp.scrublet_simulate_doublets pp.select_hvf_pegasus pp.sude pp.tsne pp.umap ``` ## Single-cell (`single`) ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: single.Annotation single.AnnotationRef single.auto_resolution single.autoResolution single.batch_correction single.CellOntologyMapper single.CellVote single.cNMF single.convert_human_to_mouse_network single.cosg single.cytotrace2 single.DCT single.DEG single.download_cellphonedb_database single.download_cl single.Drug_Response single.dynamic_features single.factor_correlation single.factor_exact single.Fate single.find_markers single.format_liana_results single.gene_trends single.generate_scRNA_report single.geneset_aucell single.get_celltype_marker single.get_cluster_celltype single.get_markers single.get_obs_value single.get_weights single.GLUE_pair single.gptcelltype single.gptcelltype_local single.hematopoiesis single.lazy single.load_human_prior_interaction_network single.MetaCell single.MetaTiME single.Monocle single.mouse_hsc_nestorowa16 single.pathway_aucell single.pathway_aucell_enrichment single.pathway_enrichment single.pathway_enrichment_plot single.plot_metacells single.pyCEFCON single.pyMOFA single.pyMOFAART single.pySCSA single.pySIMBA single.pyTOSICA single.pyVIA single.run_cellphonedb_v5 single.run_liana single.scanpy_cellanno_from_dict single.SCENIC single.TrajInfer single.Velo ``` ## Bulk RNA-seq (`bulk`) ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: bulk.batch_correction bulk.Deconvolution bulk.geneset_enrichment bulk.geneset_plot bulk.geneset_plot_multi bulk.Matrix_ID_mapping bulk.pyDEG bulk.pyGSEA bulk.pyPPI bulk.pyTCGA bulk.pyWGCNA bulk.readWGCNA bulk.string_interaction ``` ## Metabolomics (`metabol`) ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: metabol.aggregate_by_class metabol.annotate_lipids metabol.annotate_peaks metabol.anova metabol.asca metabol.asca_variance_bar metabol.biomarker_panel metabol.blank_filter metabol.corr_network metabol.corr_network_plot metabol.cv_filter metabol.dgca metabol.dgca_class_bar metabol.differential metabol.drift_correct metabol.fetch_chebi_compounds metabol.fetch_hmdb_from_name metabol.fetch_kegg_pathways metabol.fetch_lion_associations metabol.impute metabol.lion_enrichment metabol.load_pathways metabol.map_ids metabol.meba metabol.mixed_model metabol.msea_gsea metabol.msea_ora metabol.mummichog_basic metabol.normalize metabol.opls_da metabol.parse_lipid metabol.pathway_bar metabol.pathway_dot metabol.plsda metabol.pyMetabo metabol.read_lcms metabol.read_metaboanalyst metabol.read_wide metabol.roc_feature metabol.run_mofa metabol.s_plot metabol.sample_qc metabol.sample_qc_plot metabol.serrf metabol.significant_metabolites metabol.transform metabol.vip_bar metabol.vip_table metabol.volcano ``` ## Microbiome (`micro`) ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: micro.Alpha micro.ancombc micro.attach_tree micro.Beta micro.braycurtis micro.clr micro.collapse_taxa micro.combine_studies micro.conditional_probabilities micro.cooccurrence micro.DA micro.deseq2 micro.fetch_franzosa_ibd_2019 micro.filter_by_prevalence micro.fit micro.ilr micro.meta_da micro.MMvec micro.nmds micro.observed micro.Ordinate micro.paired_cca micro.paired_spearman micro.pcoa micro.plot_embedding_biplot micro.plot_mmvec_training micro.proportion_explained micro.rarefy micro.run micro.shannon micro.simulate_paired micro.top_pairs micro.wilcoxon ``` ## Spatial transcriptomics (`space`) ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: space.bin2cell space.Cal_Spatial_Net space.calculate_gene_signature space.CAST space.cellcharter space.CellLoc space.CellMap space.clusters space.create_communication_anndata space.crop_space_visium space.Deconvolution space.GASTON space.map_spatial_auto space.map_spatial_manual space.merge_cluster space.moranI space.nmf_tissue_zones space.pySpaceFlow space.pySTAGATE space.pySTAligner space.read_visium_10x space.rotate_space_visium space.salvage_secondary_labels space.spatial_autocorr space.spatial_neighbors space.STT space.svg space.sync_visium_hd_seg_geometries space.Tangram space.update_classification_from_database space.visium_10x_hd_cellpose_expand space.visium_10x_hd_cellpose_gex space.visium_10x_hd_cellpose_he ``` ## Bulk-to-Single (`bulk2single`) ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: bulk2single.Bulk2Single bulk2single.bulk2single_plot_cellprop bulk2single.bulk2single_plot_correlation bulk2single.BulkTrajBlend bulk2single.Single2Spatial ``` ## Plotting (`pl`) ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.add_density_contour pl.add_palue pl.add_pie2spatial pl.add_streamplot pl.branch_streamplot pl.bardotplot pl.boxplot pl.branch_streamplot pl.calculate_gene_density pl.ccc_heatmap pl.ccc_network_plot pl.ccc_stat_plot pl.cell_cor_heatmap pl.CellChatViz pl.cellproportion pl.complexheatmap pl.contour pl.ConvexHull pl.create_custom_colormap pl.dotplot pl.dynamic_heatmap pl.dynamic_trends pl.embedding pl.embedding_adjust pl.embedding_atlas pl.embedding_celltype pl.embedding_density pl.feature_heatmap pl.ForbiddenCity pl.gen_mpl_labels pl.geneset_wordcloud pl.group_heatmap pl.marker_heatmap pl.markers_dotplot pl.palette pl.plot1cell pl.plot_cellproportion pl.plot_ConvexHull pl.plot_embedding_celltype pl.plot_flowsig_network pl.plot_grouped_fractions pl.plot_pca_variance_ratio pl.plot_set pl.plot_spatial pl.plot_text_set pl.pyomic_palette pl.rank_genes_groups_dotplot pl.single_group_boxplot pl.stacking_vol pl.tsne pl.umap pl.venn pl.violin pl.volcano ``` ## Datasets ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: datasets.bhattacherjee datasets.blobs datasets.bm datasets.bone_marrow datasets.burczynski06 datasets.chromaffin datasets.cite_seq datasets.create_mock_dataset datasets.decov_bulk_covid_bulk datasets.decov_bulk_covid_single datasets.dentate_gyrus datasets.dentate_gyrus_scvelo datasets.download_data datasets.download_data_requests datasets.get_adata datasets.gillespie datasets.haber datasets.hematopoiesis datasets.hematopoiesis_raw datasets.hg_forebrain_glutamatergic datasets.hl60 datasets.human_tfs datasets.krumsiek11 datasets.moignard15 datasets.multi_brain_5k datasets.nascseq datasets.pancreas_cellrank datasets.pancreatic_endocrinogenesis datasets.paul15 datasets.pbmc3k datasets.pbmc8k datasets.sc_ref_Lymph_Node datasets.sceu_seq_organoid datasets.sceu_seq_rpe1 datasets.scifate datasets.scnt_seq_neuron_labeling datasets.scnt_seq_neuron_splicing datasets.scslamseq datasets.seqfish datasets.toggleswitch datasets.zebrafish ``` ## External Integrations (`external`) ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: external.GraphST ``` ## Utilities (`utils`) ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: utils.biocontext.call_tool utils.biocontext.get_ensembl_id utils.biocontext.get_fulltext utils.biocontext.get_uniprot_id utils.biocontext.list_tools utils.biocontext.query_alphafold utils.biocontext.query_cell_ontology utils.biocontext.query_chebi utils.biocontext.query_efo utils.biocontext.query_go utils.biocontext.query_hpa utils.biocontext.query_interpro utils.biocontext.query_opentargets utils.biocontext.query_panglaodb utils.biocontext.query_reactome utils.biocontext.query_string utils.biocontext.query_uniprot utils.biocontext.search_clinical_trials utils.biocontext.search_drugs utils.biocontext.search_interpro utils.biocontext.search_literature utils.biocontext.search_preprints utils.biocontext.search_pride utils.cal_paga utils.cluster utils.convert2gene_id utils.convert2gene_symbol utils.convert2symbol utils.convert_adata_for_rust utils.convert_to_pandas utils.download_CaDRReS_model utils.download_GDSC_data utils.download_geneid_annotation_pair utils.download_pathway_database utils.download_tosica_gmt utils.geneset_prepare utils.get_gene_annotation utils.gtf_to_pair_tsv utils.LDA_topic utils.load_metabolights utils.mde utils.plot_paga utils.refine_label utils.retrieve_layers utils.roe utils.store_layers utils.symbol2id utils.weighted_knn_trainer utils.weighted_knn_transfer utils.wrap_dataframe ```