# User Import dynamo as: ``` import dynamo as dyn ``` ```{eval-rst} .. currentmodule:: dynamo ``` ## Data IO ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: read read_h5ad read_loom read_h5 ``` ## Preprocessing (pp) _Preprocessor class and recipe functions_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pp.recipe_monocle pp.recipe_velocyto pp.Preprocessor pp.filter_cells_by_outliers pp.filter_cells_by_highly_variable_genes ``` _Basic preprocessing functions_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pp.filter_cells pp.filter_cells_by_outliers pp.filter_cells_by_highly_variable_genes pp.filter_cells_by_outliers pp.filter_genes_by_clusters pp.filter_genes_by_outliers pp.filter_genes_by_pattern pp.filter_genes pp.normalize_cell_expr_by_size_factors pp.scale pp.log1p pp.pca ``` _Gene selection_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pp.highest_frac_genes pp.select_genes_monocle pp.select_genes_by_pearson_residuals ``` ## Tools (tl) _kNN and moments of expressions_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: tl.neighbors tl.mnn tl.moments ``` _Kinetic parameters and RNA/protein velocity_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: tl.dynamics ``` _Labeling Velocity recipes_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: tl.recipe_deg_data tl.recipe_kin_data tl.recipe_mix_kin_deg_data tl.recipe_one_shot_data tl.velocity_N ``` _Labeling Velocity recipes_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: tl.reduceDimension tl.DDRTree tl.psl ``` _Clustering_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: tl.hdbscan tl.leiden tl.louvain tl.scc ``` _Velocity projection_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: tl.cell_velocities tl.confident_cell_velocities ``` _Velocity metrics_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: tl.cell_wise_confidence tl.gene_wise_confidence tl.pseudotime_velocity ``` _Markov chain_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: tl.generalized_diffusion_map tl.stationary_distribution tl.diffusion tl.expected_return_time ``` _Markers and differential expressions_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: tl.moran_i tl.find_group_markers tl.two_groups_degs tl.top_n_markers tl.glm_degs ``` _Cell proliferation and apoptosis_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: tl.score_cells tl.cell_growth_rate ``` _Converter and helper_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: tl.converter tl.run_scvelo tl.run_velocyto tl.vlm_to_adata ``` ## Vector field (vf) _Vector field reconstruction_ :::{note} Vector field class is internally to vf.VectorField. See our vector field classes here: [vector field](https://dynamo-release.readthedocs.io/en/latest/Class.html#vector-field) ::: ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: vf.VectorField vf.SparseVFC vf.BaseVectorField vf.SvcVectorField vf.graphize_vecfld vf.vector_field_function ``` _Vector field topology_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: vf.cluster_field vf.topography vf.FixedPoints vf.assign_fixedpoints ``` _Beyond RNA velocity_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: vf.velocities vf.speed vf.jacobian vf.divergence vf.curl vf.acceleration vf.curvature vf.torsion vf.sensitivity ``` _Beyond velocity vector field_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: vf.cell_accelerations vf.cell_curvatures ``` _Vector field ranking_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: vf.rank_genes vf.rank_expression_genes vf.rank_velocity_genes vf.rank_divergence_genes vf.rank_acceleration_genes vf.rank_curvature_genes vf.rank_jacobian_genes vf.rank_s_divergence_genes vf.rank_sensitivity_genes ``` _Single cell potential: three approaches_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: vf.gen_fixed_points vf.gen_gradient vf.IntGrad vf.DiffusionMatrix vf.action vf.Potential vf.path_integral vf.alignment vf.Wang_action vf.Wang_LAP vf.transition_rate vf.MFPT vf.Ao_pot_map vf.solveQ ``` _Stochastic processes_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: vf.diffusionMatrix ``` _Vector field clustering and graph_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: vf.cluster_field vf.streamline_clusters vf.vfGraph ``` ## Prediction (pd) ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pd.andecestor pd.fate pd.fate_bias pd.get_init_path pd.least_action pd.perturbation pd.state_graph pd.KO pd.rank_perturbation_cell_clusters pd.rank_perturbation_cells pd.rank_perturbation_genes pd.tree_model ``` ## Plotting (pl) _Preprocessing_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.basic_stats pl.show_fraction pl.feature_genes pl.biplot pl.loading pl.variance_explained pl.highest_frac_genes pl.exp_by_groups pl.bubble ``` _Cell cycle staging_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.cell_cycle_scores ``` _Scatter base_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.scatters ``` _Space plot_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.space ``` _Phase diagram: conventional scRNA-seq_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.phase_portraits ``` _Kinetic models: labeling based scRNA-seq_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.dynamics ``` _Kinetics_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.kinetic_curves pl.kinetic_heatmap pl.jacobian_kinetics pl.sensitivity_kinetics ``` _Dimension reduction_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.pca pl.tsne pl.umap pl.trimap ``` _Clustering_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.leiden pl.louvain pl.infomap pl.streamline_clusters ``` _Neighbor graph_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.nneighbors pl.state_graph ``` _Vector field plots: velocities and accelerations_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.cell_wise_vectors pl.cell_wise_vectors_3d pl.grid_vectors pl.streamline_plot pl.line_integral_conv pl.plot_energy pl.plot_3d_streamtube ``` _Vector field topology_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.plot_flow_field pl.plot_fixed_points pl.plot_fixed_points_2d pl.plot_nullclines pl.plot_separatrix pl.plot_traj pl.topography pl.response ``` _Beyond RNA velocity_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.speed pl.divergence pl.acceleration pl.curl pl.curvature pl.jacobian pl.jacobian_heatmap pl.sensitivity pl.sensitivity_heatmap ``` _Regulatory network_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.arcPlot pl.circosPlot pl.circosPlotDeprecated pl.hivePlot ``` _Potential landscape_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.show_landscape ``` _Cell fate_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.fate pl.fate_bias ``` _Heatmaps_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.causality pl.comb_logic pl.plot_hill_function pl.response ``` _Predictions_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.lap_min_time ``` _Save figures_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: pl.save_fig ``` ## Movie (mv) :::{note} animation class is internally to mv.animate_fates. See our animation classes here: [animation](https://dynamo-release.readthedocs.io/en/latest/Class.html#movie) ::: ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: mv.animate_fates ``` ## Simulation (sim) _Simple ODE vector field simulation_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: sim.toggle sim.Ying_model ``` _Gillespie simulation_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: sim.Gillespie sim.Simulator sim.state_space_sampler sim.evaluate ``` ## External (ext) ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: ext.ddhodge ext.enrichr ext.scribe ext.coexp_measure ext.scifate_glmnet ``` ## Utilities _Package versions_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: get_all_dependencies_version ``` _Clean up adata_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: cleanup ``` _Figures configuration_ ```{eval-rst} .. autosummary:: :toctree: reference/ :nosignatures: configuration.set_figure_params configuration.set_pub_style ``` [anndata]: https://anndata.readthedocs.io/en/stable/ [scanpy]: https://scanpy.readthedocs.io/en/stable/index.html [utilities]: https://scanpy.readthedocs.io/en/stable/api/index.html#reading [ray tune]: https://docs.ray.io/en/latest/tune/index.html