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dynamo-release
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  • Introduction
    • Time-resolved scRNA-seq
    • Primer on differential geometry
    • Optimal cell fate transitions via most probable path
    • In silico perturbation
  • Installation
  • Get Started
  • Tutorials
    • Preprocessing
      • Preprocessing Tutorial
      • Gene ID → Gene Symbol conversion in dynamo
    • Conventional scRNA-seq
      • Dynamo with unspliced/spliced matrix
      • Dynamo without unspliced/spliced matrix
      • Dynamo with external velocity method
    • Labeling scRNA-seq
      • scNT-seq: embryo (2C)-like stem cell
      • scNT-seq: human hematopoiesis dynamics
      • scEU-seq: cell cycle kinetic analysis
      • scEU-seq: organoid kinetic analysis
    • Differential geometry
      • Molecular mechnism: Drivers of Rapid Cell Fate Transitions
      • Molecular Interaction: Temporal Dominant Regulatory Interactions
      • Molecular Interaction: Minimal network for lineage commitment
      • Case Study: Zebrafish pigementation
    • Vector field analysis
      • Lineage: cell lineage and transition TF predictions
      • Trajectory: In silico gene perturbation
      • Shiny App
    • Multi-Velocity
      • Dynamo MultiVelo
    • Gallery
    • Tutorial gallery
      • Pancreatic endocrinogenesis
  • Frequently asked questions
  • API
    • User
      • dynamo.read
      • dynamo.read_h5ad
      • dynamo.read_loom
      • dynamo.pp.recipe_monocle
      • dynamo.pp.recipe_velocyto
      • dynamo.pp.Preprocessor
      • dynamo.pp.filter_cells_by_outliers
      • dynamo.pp.filter_cells_by_highly_variable_genes
      • dynamo.pp.filter_cells
      • dynamo.pp.filter_cells_by_outliers
      • dynamo.pp.filter_cells_by_highly_variable_genes
      • dynamo.pp.filter_cells_by_outliers
      • dynamo.pp.filter_genes_by_clusters
      • dynamo.pp.filter_genes_by_outliers
      • dynamo.pp.filter_genes_by_pattern
      • dynamo.pp.filter_genes
      • dynamo.pp.normalize_cell_expr_by_size_factors
      • dynamo.pp.scale
      • dynamo.pp.log1p
      • dynamo.pp.pca
      • dynamo.pp.highest_frac_genes
      • dynamo.pp.select_genes_monocle
      • dynamo.pp.select_genes_by_pearson_residuals
      • dynamo.tl.neighbors
      • dynamo.tl.mnn
      • dynamo.tl.moments
      • dynamo.tl.dynamics
      • dynamo.tl.recipe_deg_data
      • dynamo.tl.recipe_kin_data
      • dynamo.tl.recipe_mix_kin_deg_data
      • dynamo.tl.recipe_one_shot_data
      • dynamo.tl.velocity_N
      • dynamo.tl.reduceDimension
      • dynamo.tl.DDRTree
      • dynamo.tl.psl
      • dynamo.tl.hdbscan
      • dynamo.tl.leiden
      • dynamo.tl.louvain
      • dynamo.tl.scc
      • dynamo.tl.cell_velocities
      • dynamo.tl.confident_cell_velocities
      • dynamo.tl.cell_wise_confidence
      • dynamo.tl.gene_wise_confidence
      • dynamo.tl.pseudotime_velocity
      • dynamo.tl.generalized_diffusion_map
      • dynamo.tl.stationary_distribution
      • dynamo.tl.diffusion
      • dynamo.tl.expected_return_time
      • dynamo.tl.moran_i
      • dynamo.tl.find_group_markers
      • dynamo.tl.two_groups_degs
      • dynamo.tl.top_n_markers
      • dynamo.tl.glm_degs
      • dynamo.tl.score_cells
      • dynamo.tl.cell_growth_rate
      • dynamo.tl.converter
      • dynamo.tl.run_scvelo
      • dynamo.tl.run_velocyto
      • dynamo.tl.vlm_to_adata
      • dynamo.vf.VectorField
      • dynamo.vf.SparseVFC
      • dynamo.vf.BaseVectorField
      • dynamo.vf.SvcVectorField
      • dynamo.vf.graphize_vecfld
      • dynamo.vf.vector_field_function
      • dynamo.vf.cluster_field
      • dynamo.vf.topography
      • dynamo.vf.FixedPoints
      • dynamo.vf.assign_fixedpoints
      • dynamo.vf.velocities
      • dynamo.vf.speed
      • dynamo.vf.jacobian
      • dynamo.vf.divergence
      • dynamo.vf.curl
      • dynamo.vf.acceleration
      • dynamo.vf.curvature
      • dynamo.vf.torsion
      • dynamo.vf.sensitivity
      • dynamo.vf.cell_accelerations
      • dynamo.vf.cell_curvatures
      • dynamo.vf.rank_genes
      • dynamo.vf.rank_expression_genes
      • dynamo.vf.rank_velocity_genes
      • dynamo.vf.rank_divergence_genes
      • dynamo.vf.rank_acceleration_genes
      • dynamo.vf.rank_curvature_genes
      • dynamo.vf.rank_jacobian_genes
      • dynamo.vf.rank_s_divergence_genes
      • dynamo.vf.rank_sensitivity_genes
      • dynamo.vf.gen_fixed_points
      • dynamo.vf.gen_gradient
      • dynamo.vf.IntGrad
      • dynamo.vf.DiffusionMatrix
      • dynamo.vf.action
      • dynamo.vf.Potential
      • dynamo.vf.path_integral
      • dynamo.vf.alignment
      • dynamo.vf.Wang_action
      • dynamo.vf.Wang_LAP
      • dynamo.vf.transition_rate
      • dynamo.vf.MFPT
      • dynamo.vf.Ao_pot_map
      • dynamo.vf.solveQ
      • dynamo.vf.diffusionMatrix
      • dynamo.vf.cluster_field
      • dynamo.vf.streamline_clusters
      • dynamo.vf.vfGraph
      • dynamo.pd.andecestor
      • dynamo.pd.fate
      • dynamo.pd.fate_bias
      • dynamo.pd.get_init_path
      • dynamo.pd.least_action
      • dynamo.pd.perturbation
      • dynamo.pd.state_graph
      • dynamo.pd.KO
      • dynamo.pd.rank_perturbation_cell_clusters
      • dynamo.pd.rank_perturbation_cells
      • dynamo.pd.rank_perturbation_genes
      • dynamo.pd.tree_model
      • dynamo.pl.basic_stats
      • dynamo.pl.show_fraction
      • dynamo.pl.feature_genes
      • dynamo.pl.biplot
      • dynamo.pl.loading
      • dynamo.pl.variance_explained
      • dynamo.pl.highest_frac_genes
      • dynamo.pl.exp_by_groups
      • dynamo.pl.bubble
      • dynamo.pl.cell_cycle_scores
      • dynamo.pl.scatters
      • dynamo.pl.space
      • dynamo.pl.phase_portraits
      • dynamo.pl.dynamics
      • dynamo.pl.kinetic_curves
      • dynamo.pl.kinetic_heatmap
      • dynamo.pl.jacobian_kinetics
      • dynamo.pl.sensitivity_kinetics
      • dynamo.pl.pca
      • dynamo.pl.tsne
      • dynamo.pl.umap
      • dynamo.pl.trimap
      • dynamo.pl.leiden
      • dynamo.pl.louvain
      • dynamo.pl.infomap
      • dynamo.pl.streamline_clusters
      • dynamo.pl.nneighbors
      • dynamo.pl.state_graph
      • dynamo.pl.cell_wise_vectors
      • dynamo.pl.cell_wise_vectors_3d
      • dynamo.pl.grid_vectors
      • dynamo.pl.streamline_plot
      • dynamo.pl.line_integral_conv
      • dynamo.pl.plot_energy
      • dynamo.pl.plot_3d_streamtube
      • dynamo.pl.plot_flow_field
      • dynamo.pl.plot_fixed_points
      • dynamo.pl.plot_fixed_points_2d
      • dynamo.pl.plot_nullclines
      • dynamo.pl.plot_separatrix
      • dynamo.pl.plot_traj
      • dynamo.pl.topography
      • dynamo.pl.response
      • dynamo.pl.speed
      • dynamo.pl.divergence
      • dynamo.pl.acceleration
      • dynamo.pl.curl
      • dynamo.pl.curvature
      • dynamo.pl.jacobian
      • dynamo.pl.jacobian_heatmap
      • dynamo.pl.sensitivity
      • dynamo.pl.sensitivity_heatmap
      • dynamo.pl.arcPlot
      • dynamo.pl.circosPlot
      • dynamo.pl.circosPlotDeprecated
      • dynamo.pl.hivePlot
      • dynamo.pl.show_landscape
      • dynamo.pl.fate
      • dynamo.pl.fate_bias
      • dynamo.pl.causality
      • dynamo.pl.comb_logic
      • dynamo.pl.plot_hill_function
      • dynamo.pl.response
      • dynamo.pl.lap_min_time
      • dynamo.pl.save_fig
      • dynamo.mv.animate_fates
      • dynamo.sim.toggle
      • dynamo.sim.Ying_model
      • dynamo.sim.Gillespie
      • dynamo.sim.Simulator
      • dynamo.sim.state_space_sampler
      • dynamo.sim.evaluate
      • dynamo.ext.ddhodge
      • dynamo.ext.enrichr
      • dynamo.ext.scribe
      • dynamo.ext.coexp_measure
      • dynamo.ext.scifate_glmnet
      • dynamo.get_all_dependencies_version
      • dynamo.cleanup
      • dynamo.configuration.set_figure_params
      • dynamo.configuration.set_pub_style
    • Datasets
      • dynamo.sample_data.scNT_seq_neuron_splicing
      • dynamo.sample_data.scNT_seq_neuron_labeling
      • dynamo.sample_data.zebrafish
      • dynamo.sample_data.DentateGyrus
      • dynamo.sample_data.Haber
      • dynamo.sample_data.hgForebrainGlutamatergic
      • dynamo.sample_data.chromaffin
      • dynamo.sample_data.BM
      • dynamo.sample_data.pancreatic_endocrinogenesis
      • dynamo.sample_data.DentateGyrus_scvelo
      • dynamo.sample_data.scEU_seq_rpe1
      • dynamo.sample_data.scEU_seq_organoid
      • dynamo.sample_data.hematopoiesis
      • dynamo.sample_data.hematopoiesis_raw
  • Contributing to dynamo
  • Release Notes
  • References
  • Discussion
  • GitHub
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Preprocessing¶

  • Preprocessing Tutorial
  • Gene ID → Gene Symbol conversion in dynamo
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