Index

_

__init__() (dynamo.vf.base_vectorfield method) (dynamo.vf.svc_vectorfield method) (dynamo.vf.vfGraph method)

A

acceleration() (in module dynamo.vf) action() (in module dynamo.vf)

alignment() (in module dynamo.vf) animate_fates() (in module dynamo.mv) Ao_pot_map() (in module dynamo.vf)

B

base_vectorfield (class in dynamo.vf)

basic_stats() (in module dynamo.pl)

C

cell_accelerations() (in module dynamo.vf) cell_curvatures() (in module dynamo.vf) cell_cycle_scores() (in module dynamo.pl) (in module dynamo.pp) cell_growth_rate() (in module dynamo.tl) cell_velocities() (in module dynamo.tl) cell_wise_confidence() (in module dynamo.tl) cell_wise_vectors() (in module dynamo.pl) cleanup() (in module dynamo)

cluster_field() (in module dynamo.tl) coexp_measure() (in module dynamo.ext) concatenate_data() (dynamo.est.csc.ss_estimation method) confident_cell_velocities() (in module dynamo.tl) converter() (in module dynamo.tl) curl() (in module dynamo.pl) (in module dynamo.vf) curvature() (in module dynamo.pl) (in module dynamo.vf)

D

ddhodge() (in module dynamo.ext) DDRTree() (in module dynamo.tl) diffusion() (in module dynamo.tl) DiffusionMatrix() (in module dynamo.vf) diffusionMatrix() (in module dynamo.vf)

divergence() (in module dynamo.pl) (in module dynamo.vf) dynamics() (in module dynamo.pl) (in module dynamo.tl) dynamo module

E

enrichr() (in module dynamo.ext) Estimation_DeterministicDeg (class in dynamo.est.tsc) Estimation_DeterministicDegNosp (class in dynamo.est.tsc) Estimation_DeterministicKin (class in dynamo.est.tsc) Estimation_DeterministicKinNosp (class in dynamo.est.tsc) Estimation_MomentDeg (class in dynamo.est.tsc)

Estimation_MomentDegNosp (class in dynamo.est.tsc) Estimation_MomentKin (class in dynamo.est.tsc) Estimation_MomentKinNosp (class in dynamo.est.tsc) evaluate() (in module dynamo.sim) exp_by_groups() (in module dynamo.pl) expected_return_time() (in module dynamo.tl)

F

fate() (in module dynamo.pd) fate_bias() (in module dynamo.pd) (in module dynamo.pl) feature_genes() (in module dynamo.pl) find_group_markers() (in module dynamo.tl) fit() (dynamo.est.csc.ss_estimation method) (dynamo.vf.Pot method) fit_alpha_oneshot() (dynamo.est.csc.ss_estimation method) fit_beta_gamma_lsq() (dynamo.est.csc.ss_estimation method) fit_gamma_nosplicing_lsq() (dynamo.est.csc.ss_estimation method) fit_gamma_steady_state() (dynamo.est.csc.ss_estimation method)

fit_gamma_stochastic() (dynamo.est.csc.ss_estimation method) fit_lsq() (dynamo.est.tsc.Estimation_DeterministicDeg method) (dynamo.est.tsc.Estimation_DeterministicDegNosp method) (dynamo.est.tsc.Estimation_DeterministicKin method) (dynamo.est.tsc.Estimation_DeterministicKinNosp method) (dynamo.est.tsc.Estimation_MomentDeg method) (dynamo.est.tsc.Estimation_MomentDegNosp method) (dynamo.est.tsc.Estimation_MomentKin method) (dynamo.est.tsc.Estimation_MomentKinNosp method) (dynamo.est.tsc.kinetic_estimation method) (dynamo.est.tsc.Lambda_NoSwitching method) (dynamo.est.tsc.Mixture_KinDeg_NoSwitching method)

G

gen_fixed_points() (in module dynamo.vf) gen_gradient() (in module dynamo.vf) gene_wise_confidence() (in module dynamo.tl) generalized_diffusion_map() (in module dynamo.tl) get_all_dependencies_version() (in module dynamo) get_exist_data_names() (dynamo.est.csc.ss_estimation method)

get_n_cells() (dynamo.est.csc.velocity method) get_n_genes() (dynamo.est.csc.ss_estimation method) (dynamo.est.csc.velocity method) Gillespie() (in module dynamo.sim) glm_degs() (in module dynamo.tl) grid_vectors() (in module dynamo.pl)

H

hdbscan() (in module dynamo.tl)

I

IntGrad() (in module dynamo.vf)

J

jacobian() (in module dynamo.pl)

jacobian_heatmap() (in module dynamo.pl) jacobian_kinetics() (in module dynamo.pl)

K

kinetic_curves() (in module dynamo.pl)

kinetic_estimation (class in dynamo.est.tsc) kinetic_heatmap() (in module dynamo.pl)

L

Lambda_NoSwitching (class in dynamo.est.tsc)

line_integral_conv() (in module dynamo.pl)

M

MFPT() (in module dynamo.vf) Mixture_KinDeg_NoSwitching (class in dynamo.est.tsc) mnn() (in module dynamo.tl)

module dynamo moments() (in module dynamo.tl) moran_i() (in module dynamo.tl)

N

neighbors() (in module dynamo.tl)

neurogenesis() (in module dynamo.sim) nneighbors() (in module dynamo.pl)

P

path_integral() (in module dynamo.vf) pca() (in module dynamo.pl) phase_portraits() (in module dynamo.pl) plot_energy() (in module dynamo.pl) plot_fixed_points() (in module dynamo.pl) plot_flow_field() (in module dynamo.pl)

plot_nullclines() (in module dynamo.pl) plot_separatrix() (in module dynamo.pl) plot_traj() (in module dynamo.pl) Pot (class in dynamo.vf) Potential() (in module dynamo.vf) psl() (in module dynamo.tl)

R

rank_acceleration_genes() (in module dynamo.vf) rank_curvature_genes() (in module dynamo.vf) rank_divergence_genes() (in module dynamo.vf) rank_velocity_genes() (in module dynamo.vf)

read() (in module dynamo) read_h5ad() (in module dynamo) read_loom() (in module dynamo) recipe_monocle() (in module dynamo.pp) reduceDimension() (in module dynamo.tl)

S

save_fig() (in module dynamo.pl) scatters() (in module dynamo.pl) scifate_glmnet() (in module dynamo.ext) score_cells() (in module dynamo.tl) scribe() (in module dynamo.ext) set_figure_params() (in module dynamo.configuration) set_parameter() (dynamo.est.csc.ss_estimation method) set_pub_style() (in module dynamo.configuration) show_fraction() (in module dynamo.pl) show_landscape() (in module dynamo.pl) Simulator() (in module dynamo.sim) solve_alpha_mix_std_stm() (dynamo.est.csc.ss_estimation method)

solveQ() (in module dynamo.vf) SparseVFC() (in module dynamo.vf) speed() (in module dynamo.pl) (in module dynamo.vf) ss_estimation (class in dynamo.est.csc) state_graph() (in module dynamo.pd) (in module dynamo.pl) state_space_sampler() (in module dynamo.sim) stationary_distribution() (in module dynamo.tl) StreamFuncAnim (class in dynamo.mv) streamline_plot() (in module dynamo.pl) svc_vectorfield (class in dynamo.vf)

T

test_chi2() (dynamo.est.tsc.Estimation_DeterministicDeg method) (dynamo.est.tsc.Estimation_DeterministicDegNosp method) (dynamo.est.tsc.Estimation_DeterministicKin method) (dynamo.est.tsc.Estimation_DeterministicKinNosp method) (dynamo.est.tsc.Estimation_MomentDeg method) (dynamo.est.tsc.Estimation_MomentDegNosp method) (dynamo.est.tsc.Estimation_MomentKin method) (dynamo.est.tsc.Estimation_MomentKinNosp method) (dynamo.est.tsc.kinetic_estimation method) (dynamo.est.tsc.Lambda_NoSwitching method) (dynamo.est.tsc.Mixture_KinDeg_NoSwitching method)

toggle() (in module dynamo.sim) top_n_markers() (in module dynamo.tl) topography() (in module dynamo.pl) (in module dynamo.vf) torsion() (in module dynamo.vf) transition_rate() (in module dynamo.vf) trimap() (in module dynamo.pl) tsne() (in module dynamo.pl) two_genes_motif() (in module dynamo.sim) two_groups_degs() (in module dynamo.tl)

U

umap() (in module dynamo.pl)

update() (dynamo.mv.StreamFuncAnim method)

V

variance_explained() (in module dynamo.pl) vel_p() (dynamo.est.csc.velocity method) vel_s() (dynamo.est.csc.velocity method)

vel_u() (dynamo.est.csc.velocity method) velocities() (in module dynamo.vf) velocity (class in dynamo.est.csc) vfGraph (class in dynamo.vf)

W

Wang_action() (in module dynamo.vf)

Wang_LAP() (in module dynamo.vf)

Y

Ying_model() (in module dynamo.sim)