.. automodule:: dynamo
Import dynamo as:
import dynamo as dyn
(See more at anndata-docs)
.. autosummary:: :toctree: _autosummary read read_h5ad read_loom
.. autosummary::
:toctree: _autosummary
pp.recipe_monocle
pp.cell_cycle_scores
.. pp.pca
Note
Classes in est are internally to Tools. See our estimation classes here: estimation
kNN and moments of expressions
.. autosummary::
:toctree: _autosummary
tl.neighbors
tl.mnn
tl.moments
Kinetic parameters and RNA/protein velocity
.. autosummary::
:toctree: _autosummary
tl.dynamics
.. tl.calc_1nd_moment
.. tl.calc_2nd_moment
Dimension reduction
.. autosummary::
:toctree: _autosummary
tl.reduceDimension
tl.DDRTree
tl.psl
.. tl.cal_ncenter
Clustering
.. autosummary::
:toctree: _autosummary
tl.hdbscan
tl.cluster_field
Velocity projection
.. autosummary::
:toctree: _autosummary
tl.cell_velocities
tl.confident_cell_velocities
Velocity metrics
.. autosummary::
:toctree: _autosummary
tl.cell_wise_confidence
tl.gene_wise_confidence
Markov chain
.. autosummary::
:toctree: _autosummary
tl.generalized_diffusion_map
tl.stationary_distribution
tl.diffusion
tl.expected_return_time
.. tl.markov_combination
.. tl.compute_markov_trans_prob
.. tl.compute_kernel_trans_prob
.. tl.compute_drift_kernel
.. tl.compute_drift_local_kernel
.. tl.compute_density_kernel
.. tl.makeTransitionMatrix
.. tl.compute_tau
.. tl.MarkovChain
.. tl.KernelMarkovChain
.. tl.DiscreteTimeMarkovChain
.. tl.ContinuousTimeMarkovChain
Markers and differential expressions
.. autosummary::
:toctree: _autosummary
tl.moran_i
tl.find_group_markers
tl.two_groups_degs
tl.top_n_markers
tl.glm_degs
.. tl.TRNET
.. tl.trn
.. tl.sample_by_velocity
.. tl.lhsclassic
.. tl.sample
Cell proliferation and apoptosis
.. autosummary::
:toctree: _autosummary
tl.score_cells
tl.cell_growth_rate
.. tl.n_descendants
.. tl.growth_rate
Converter
.. autosummary::
:toctree: _autosummary
tl.converter
Vector field reconstruction
Note
Vector field class is internally to vf.VectorField. See our vector field classes here: vector field
.. autosummary::
:toctree: _autosummary
vf.SparseVFC
vf.base_vectorfield
vf.SvcVectorfield
.. vf.graphize_vecfld
.. vf.vector_field_function
Vector field topology
.. autosummary::
:toctree: _autosummary
vf.topography
.. vf.FixedPoints
.. vf.VectorField2D
Beyond RNA velocity
.. autosummary::
:toctree: _autosummary
vf.velocities
vf.speed
vf.divergence
vf.curl
vf.acceleration
vf.curvature
vf.torsion
Beyond velocity vector field
.. autosummary::
:toctree: _autosummary
vf.cell_accelerations
vf.cell_curvatures
Vector field ranking
.. autosummary::
:toctree: _autosummary
vf.rank_velocity_genes
vf.rank_divergence_genes
vf.rank_acceleration_genes
vf.rank_curvature_genes
Single cell potential: three approaches
.. autosummary::
:toctree: _autosummary
vf.gen_fixed_points
vf.gen_gradient
vf.IntGrad
vf.DiffusionMatrix
vf.action
vf.Potential
.. vf.search_fixed_points
vf.path_integral
vf.alignment
vf.Wang_action
vf.Wang_LAP
vf.transition_rate
vf.MFPT
vf.Ao_pot_map
vf.solveQ
Stochastic processes
.. autosummary::
:toctree: _autosummary
vf.diffusionMatrix
.. autosummary:: :toctree: _autosummary
Vector field lineage fate
pd.fate pd.fate_bias
Vector field state graph
.. autosummary::
:toctree: _autosummary
pd.state_graph
Preprocessing
.. autosummary::
:toctree: _autosummary
pl.basic_stats
pl.show_fraction
pl.feature_genes
pl.variance_explained
pl.exp_by_groups
Cell cycle staging
.. autosummary::
:toctree: _autosummary
pl.cell_cycle_scores
Scatter base
.. autosummary::
:toctree: _autosummary
pl.scatters
Phase diagram: conventional scRNA-seq
.. autosummary::
:toctree: _autosummary
pl.phase_portraits
Kinetic models: labeling based scRNA-seq
.. autosummary::
:toctree: _autosummary
pl.dynamics
Kinetics
.. autosummary::
:toctree: _autosummary
pl.kinetic_curves
pl.kinetic_heatmap
pl.jacobian_kinetics
Dimension reduction
.. autosummary::
:toctree: _autosummary
pl.pca
pl.tsne
pl.umap
pl.trimap
Neighbor graph
.. autosummary::
:toctree: _autosummary
pl.nneighbors
pl.state_graph
Vector field plots: velocities and accelerations
.. autosummary::
:toctree: _autosummary
pl.cell_wise_vectors
pl.grid_vectors
pl.streamline_plot
pl.line_integral_conv
pl.plot_energy
Vector field topology
.. autosummary::
:toctree: _autosummary
pl.plot_flow_field
pl.plot_fixed_points
pl.plot_nullclines
pl.plot_separatrix
pl.plot_traj
pl.topography
Beyond RNA velocity
.. autosummary::
:toctree: _autosummary
pl.speed
pl.divergence
pl.curl
pl.curvature
pl.jacobian
pl.jacobian_heatmap
Potential landscape
.. autosummary::
:toctree: _autosummary
pl.show_landscape
Cell fate
.. autosummary::
:toctree: _autosummary
pl.fate_bias
Save figures
.. autosummary::
:toctree: _autosummary
pl.save_fig
Note
animation class is internally to mv.animate_fates. See our animation classes here: animation
.. autosummary:: :toctree: _autosummary mv.animate_fates
.. autosummary:: :toctree: _autosummary
Simple ODE vector field simulation
.. autosummary::
:toctree: _autosummary
sim.two_genes_motif
sim.neurogenesis
sim.toggle
sim.Ying_model
Gillespie simulation
.. autosummary::
:toctree: _autosummary
sim.Gillespie
sim.Simulator
sim.state_space_sampler
sim.evaluate
.. autosummary::
:toctree: _autosummary
ext.ddhodge
ext.enrichr
ext.scribe
ext.coexp_measure
ext.scifate_glmnet
Package versions
.. autosummary::
:toctree: _autosummary
get_all_dependencies_version
Clean up adata
.. autosummary::
:toctree: _autosummary
cleanup
Figures configuration
.. autosummary:: :toctree: _autosummary configuration.set_figure_params configuration.set_pub_style