cell2fate
latest
Installation
Quick start tutorial:
Cell2Fate analysis of mouse pancreas development dataset
Assessing confidence in cell2fate predictions
Cell2Fate + Cell2Location:
Running cell2fate and saving modules in human developing brain dataset
Running cell2location with the saved modules from the human developing brain dataset
Reproduce publication figures:
Cell2Fate analysis of mouse bone marrow dataset
Cell2Fate dynamical model analysis of PBMC dataset
Cell2Fate analysis of human bone marrow dataset
Cell2Fate analysis of mouse erythroid dataset
Cell2Fate analysis of mouse dentate gyrus dataset
API:
Prepare data
Cell2Fate: RNA velocity (scvi-tools/pyro)
Plotting
General utils
Pyro and scvi-tools infrastructure classes
cell2fate
Index
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Index
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C
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E
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F
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W
A
AutoAmortisedHierarchicalNormalMessenger (class in cell2fate.AutoAmortisedNormalMessenger)
AutoGuideMixinModule (class in cell2fate._pyro_mixin)
C
call_new() (cell2fate._pyro_mixin.MyAutoHierarchicalNormalMessenger method)
cell2fate._pyro_mixin
module
cell2fate.AutoAmortisedNormalMessenger
module
Cell2fate_DynamicalModel (class in cell2fate)
Cell2fate_DynamicalModel_module (class in cell2fate._cell2fate_DynamicalModel_module)
Cell2FateBaseModule (class in cell2fate._pyro_base_cell2fate_module)
change_requires_grad() (cell2fate._pyro_mixin.PyroAggressiveTrainingPlan1 method)
compare_module_activation() (cell2fate.Cell2fate_DynamicalModel method)
complete_tensor_along_dim() (in module cell2fate._pyro_mixin)
compute_and_plot_module_velocity() (cell2fate.Cell2fate_DynamicalModel method)
compute_and_plot_total_velocity() (cell2fate.Cell2fate_DynamicalModel method)
compute_and_plot_total_velocity_scvelo() (cell2fate.Cell2fate_DynamicalModel method)
compute_module_summary_statistics() (cell2fate.Cell2fate_DynamicalModel method)
compute_velocity_graph_Bergen2020() (cell2fate.Cell2fate_DynamicalModel method)
(cell2fate.utils method)
create_plates() (cell2fate._cell2fate_DynamicalModel_module.Cell2fate_DynamicalModel_module method)
E
encode() (cell2fate.AutoAmortisedNormalMessenger.AutoAmortisedHierarchicalNormalMessenger method)
expand_zeros_along_dim() (in module cell2fate._pyro_mixin)
export_posterior() (cell2fate.Cell2fate_DynamicalModel method)
export_posterior_quantiles() (cell2fate.Cell2fate_DynamicalModel method)
F
FCLayersPyro (class in cell2fate.AutoAmortisedNormalMessenger)
forward() (cell2fate._cell2fate_DynamicalModel_module.Cell2fate_DynamicalModel_module method)
G
G_a() (cell2fate.utils method)
G_b() (cell2fate.utils method)
get_max_modules() (cell2fate.utils method)
get_module_top_features() (cell2fate.Cell2fate_DynamicalModel method)
get_posterior() (cell2fate.AutoAmortisedNormalMessenger.AutoAmortisedHierarchicalNormalMessenger method)
get_posterior_quantile() (cell2fate._pyro_mixin.MyAutoHierarchicalNormalMessenger method)
get_training_data() (cell2fate.utils method)
guide (cell2fate._pyro_base_cell2fate_module.Cell2FateBaseModule property)
I
init_to_value() (cell2fate._pyro_base_cell2fate_module.Cell2FateBaseModule method)
(in module cell2fate._pyro_mixin)
is_amortised (cell2fate._pyro_base_cell2fate_module.Cell2FateBaseModule property)
L
list_obs_plate_vars (cell2fate._pyro_base_cell2fate_module.Cell2FateBaseModule property)
list_obs_plate_vars() (cell2fate._cell2fate_DynamicalModel_module.Cell2fate_DynamicalModel_module method)
M
median() (cell2fate.AutoAmortisedNormalMessenger.AutoAmortisedHierarchicalNormalMessenger method)
model (cell2fate._pyro_base_cell2fate_module.Cell2FateBaseModule property)
module
cell2fate._pyro_mixin
cell2fate.AutoAmortisedNormalMessenger
mu_alpha() (cell2fate.utils method)
mu_mRNA_continousAlpha_globalTime_twoStates() (cell2fate.utils method)
mu_mRNA_continuousAlpha() (cell2fate.utils method)
MyAutoHierarchicalNormalMessenger (class in cell2fate._pyro_mixin)
P
plot_genes() (cell2fate.Cell2fate_DynamicalModel method)
plot_history() (cell2fate.Cell2fate_DynamicalModel method)
plot_module_summary_statistics() (cell2fate.Cell2fate_DynamicalModel method)
plot_technical_variables() (cell2fate.Cell2fate_DynamicalModel method)
plot_top_features() (cell2fate.Cell2fate_DynamicalModel method)
plot_velocity_umap_Bergen2020() (cell2fate.utils method)
posterior_quantile() (cell2fate._pyro_mixin.QuantileMixin method)
PyroAggressiveTrainingPlan1 (class in cell2fate._pyro_mixin)
PyroTrainingPlan_ClippedAdamDecayingRate (class in cell2fate._pyro_mixin)
Q
QuantileMixin (class in cell2fate._pyro_mixin)
quantiles() (cell2fate._pyro_mixin.MyAutoHierarchicalNormalMessenger method)
(cell2fate.AutoAmortisedNormalMessenger.AutoAmortisedHierarchicalNormalMessenger method)
R
robust_optimization() (cell2fate.utils method)
S
setup_anndata() (cell2fate.Cell2fate_DynamicalModel class method)
T
train() (cell2fate.Cell2fate_DynamicalModel method)
training (cell2fate._cell2fate_DynamicalModel_module.Cell2fate_DynamicalModel_module attribute)
(cell2fate._pyro_base_cell2fate_module.Cell2FateBaseModule attribute)
(cell2fate._pyro_mixin.MyAutoHierarchicalNormalMessenger attribute)
(cell2fate._pyro_mixin.PyroAggressiveTrainingPlan1 attribute)
(cell2fate._pyro_mixin.PyroTrainingPlan_ClippedAdamDecayingRate attribute)
(cell2fate.AutoAmortisedNormalMessenger.AutoAmortisedHierarchicalNormalMessenger attribute)
(cell2fate.AutoAmortisedNormalMessenger.FCLayersPyro attribute)
training_epoch_end() (cell2fate._pyro_mixin.PyroAggressiveTrainingPlan1 method)
training_step() (cell2fate._pyro_mixin.PyroAggressiveTrainingPlan1 method)
V
view_history() (cell2fate.Cell2fate_DynamicalModel method)
visualize_module_trajectories() (cell2fate.Cell2fate_DynamicalModel method)
W
weight_type (cell2fate.AutoAmortisedNormalMessenger.AutoAmortisedHierarchicalNormalMessenger attribute)