Index _ | A | B | C | D | E | F | G | H | I | L | M | N | P | R | S | T | U | V | W _ __init__() (stereo.algorithm.cell_pose.Cellpose method) (stereo.core.ms_data.MSData method) (stereo.core.StereoExpData method) (stereo.core.StPipeline method) (stereo.image.tissue_cut.RNATissueCut method), [1] (stereo.image.tissue_cut.SingleStrandDNATissueCut method), [1] A adjusted_rand_score() (stereo.core.StPipeline method) anndata_to_stereo() (in module stereo.io) annotation() (stereo.core.StPipeline method) auc_heatmap() (stereo.algorithm.regulatory_network_inference.PlotRegulatoryNetwork method) auc_heatmap_by_group() (stereo.algorithm.regulatory_network_inference.PlotRegulatoryNetwork method) B boxplot_transit_gene() (stereo.plots.PlotTimeSeries method) C cal_qc() (stereo.core.StPipeline method) ccc_circos_plot() (stereo.algorithm.cell_cell_communication.PlotCellCellCommunication method) ccc_dot_plot() (stereo.algorithm.cell_cell_communication.PlotCellCellCommunication method) ccc_heatmap() (stereo.algorithm.cell_cell_communication.PlotCellCellCommunication method) ccc_sankey_plot() (stereo.algorithm.cell_cell_communication.PlotCellCellCommunication method) cell_correct() (in module stereo.tools.cell_correct) cell_cut() (stereo.tools.cell_cut.CellCut method) cell_seg() (in module stereo.image.segmentation.segment) cell_seg_deepcell() (in module stereo.image.segmentation_deepcell.segment) cells_plotting() (stereo.plots.PlotCollection method) center_align() (in module stereo.algorithm.paste) cluster_bins_to_cellbins() (in module stereo.utils) cluster_scatter() (stereo.plots.PlotCollection method) clusters_genes_heatmap() (stereo.plots.ClustersGenesHeatmap method) clusters_genes_scatter() (stereo.plots.ClustersGenesScatter method) co_occurrence_heatmap() (stereo.plots.PlotCoOccurrence method) co_occurrence_plot() (stereo.plots.PlotCoOccurrence method) create_pyramid() (in module stereo.image.pyramid) D dendrogram() (stereo.plots.PlotDendrogram method) E elbow() (stereo.plots.PlotElbow method) F filter_by_clusters() (stereo.core.StPipeline method) filter_by_hvgs() (stereo.core.StPipeline method) filter_cells() (stereo.core.StPipeline method) filter_coordinates() (stereo.core.StPipeline method) filter_genes() (stereo.core.StPipeline method) find_marker_genes() (stereo.core.StPipeline method) fuzz_cluster_plot() (stereo.plots.PlotTimeSeries method) G gaussian_smooth() (stereo.core.StPipeline method) gaussian_smooth_scatter_by_gene() (stereo.plots.PlotCollection method) genes_count() (stereo.plots.PlotCollection method) grn_dotplot() (stereo.algorithm.regulatory_network_inference.PlotRegulatoryNetwork method) H highly_variable_genes() (stereo.core.StPipeline method) (stereo.plots.PlotCollection method) hotspot_local_correlations() (stereo.plots.PlotCollection method) hotspot_modules() (stereo.plots.PlotCollection method) I interact_annotation_cluster() (stereo.plots.PlotCollection method) interact_cluster() (stereo.plots.PlotCollection method) interact_spatial_scatter() (stereo.plots.PlotCollection method) L leiden() (stereo.core.StPipeline method) log1p() (stereo.core.StPipeline method) louvain() (stereo.core.StPipeline method) M main() (stereo.algorithm.batch_qc.BatchQc method) (stereo.algorithm.cell_cell_communication.CellCellCommunication method) (stereo.algorithm.co_occurrence.CoOccurrence method) (stereo.algorithm.community_detection.CommunityDetection method) (stereo.algorithm.dendrogram.Dendrogram method) (stereo.algorithm.gen_ccc_micro_envs.GenCccMicroEnvs method) (stereo.algorithm.get_niche.GetNiche method) (stereo.algorithm.paste.Paste method) (stereo.algorithm.regulatory_network_inference.RegulatoryNetworkInference method) (stereo.algorithm.single_r.SingleR method) (stereo.algorithm.time_series_analysis.TimeSeriesAnalysis method) marker_genes_heatmap() (stereo.plots.PlotCollection method) marker_genes_scatter() (stereo.plots.PlotCollection method) marker_genes_text() (stereo.plots.PlotCollection method) marker_genes_volcano() (stereo.plots.PlotCollection method) merge() (in module stereo.utils.data_helper) merge_pyramid() (in module stereo.image.pyramid) module stereo, [1], [2], [3], [4], [5], [6] stereo.plt ms_paga_time_series_plot() (stereo.plots.PlotTimeSeriesAnalysis method) MSData (class in stereo.core.ms_data) N neighbors() (stereo.core.StPipeline method) normalize_total() (stereo.core.StPipeline method) P paga_compare() (stereo.plots.PlotPaga method) paga_plot() (stereo.plots.PlotPaga method) paga_time_series_plot() (stereo.plots.PlotTimeSeries method) pairwise_align() (in module stereo.algorithm.paste) pca() (stereo.core.StPipeline method) phenograph() (stereo.core.StPipeline method) plot_genes_in_pseudotime() (stereo.plots.PlotGenesInPseudotime method) plot_time_scatter() (stereo.plots.PlotVec method) plot_vec() (stereo.plots.PlotVec method) plot_vec_3d() (stereo.plots.PlotVec3D method) R raw_checkpoint() (stereo.core.StPipeline method) read_ann_h5ad() (in module stereo.io) read_gef() (in module stereo.io) read_gef_info() (in module stereo.io) read_gem() (in module stereo.io) read_h5ad() (in module stereo.io) read_h5ms() (in module stereo.io) read_seurat_h5ad() (in module stereo.io) read_stereo_h5ad() (in module stereo.io) RNATissueCut (class in stereo.image.tissue_cut) S scale() (stereo.core.StPipeline method) sctransform() (stereo.core.StPipeline method) silhouette_score() (stereo.core.StPipeline method) SingleStrandDNATissueCut (class in stereo.image.tissue_cut) spatial_hotspot() (stereo.core.StPipeline method) spatial_neighbors() (stereo.core.StPipeline method) spatial_scatter() (stereo.plots.PlotCollection method) spatial_scatter_by_gene() (stereo.plots.PlotCollection method) spatial_scatter_by_regulon() (stereo.algorithm.regulatory_network_inference.PlotRegulatoryNetwork method) spatial_scatter_by_regulon_3D() (stereo.algorithm.regulatory_network_inference.PlotRegulatoryNetwork method) split() (in module stereo.utils.data_helper) stereo module, [1], [2], [3], [4], [5], [6] stereo.plt module stereo_to_anndata() (in module stereo.io) StereoExpData (class in stereo.core) StPipeline (class in stereo.core) T time_series_tree_plot() (stereo.plots.PlotTimeSeriesAnalysis method) tissue_extraction_to_bgef() (in module stereo.tools.tissue_extraction) to_integrate() (stereo.core.ms_data.MSData method) to_isolated() (stereo.core.ms_data.MSData method) TVG_volcano_plot() (stereo.plots.PlotTimeSeries method) U umap() (stereo.core.StPipeline method) (stereo.plots.PlotCollection method) update_gef() (in module stereo.io) V violin() (stereo.plots.PlotCollection method) W write_h5ad() (in module stereo.io) write_h5ms() (in module stereo.io) write_mid_gef() (in module stereo.io)