dynamo
v0.95.1
Contents
10 minutes to dynamo
API
Class
Release notes
Reference
Acknowledgement
Main tutorials
Zebrafish pigmentation
Other tutorials
Pancreatic endocrinogenesis
Dentate gyrus dataset
dynamo
»
Index
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Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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P
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R
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S
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T
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U
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V
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W
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Y
_
__init__() (dynamo.mv.StreamFuncAnim 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
basic_stats() (in module dynamo.pl)
C
cell_accelerations() (in module dynamo.vf)
cell_cycle_scores() (in module dynamo.pl)
(in module dynamo.pp)
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)
concatenate_data() (dynamo.est.csc.ss_estimation method)
confident_cell_velocities() (in module dynamo.tl)
converter() (in module dynamo.tl)
csc.ss_estimation (class in dynamo.est)
csc.velocity (class in dynamo.est)
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
evaluate() (dynamo.vf.vectorfield method)
(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.vectorfield 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_Jacobian() (dynamo.vf.vectorfield 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_heatmap() (in module dynamo.pl)
L
line_integral_conv() (in module dynamo.pl)
M
MFPT() (in module dynamo.vf)
mnn() (in module dynamo.tl)
module
dynamo
moments() (in module dynamo.tl)
moran_i() (in module dynamo.tl)
mutual_inform() (in module dynamo.ext)
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)
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_speed_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)
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)
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)
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)
tsc.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.kinetic_estimation (class in dynamo.est)
tsc.Lambda_NoSwitching (class in dynamo.est)
tsc.Mixture_KinDeg_NoSwitching (class in dynamo.est)
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)
V
variance_explained() (in module dynamo.pl)
vectorfield (class in dynamo.vf)
VectorField() (in module dynamo.vf)
vel_p() (dynamo.est.csc.velocity method)
vel_s() (dynamo.est.csc.velocity method)
vel_u() (dynamo.est.csc.velocity method)
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)
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