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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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Gallery¶

Tutorial gallery¶

Welcome to the dynamo tutorial gallery. If you have any new analysis results worth sharing by applying dynamo to your dataset, welcome to let us know on GitHub or via email and we can put them in this gallery.

Pancreatic endocrinogenesis analysis

  • Pancreatic endocrinogenesis
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Pancreatic endocrinogenesis
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