Package index • CellODE

All functions

CellODE-package CellODE: CellODE: Cellular Dynamics Inference Using Neural ODE

MakeDataset(): Create Dataset for Training

TNODE(): Time Neural ODE (TNODE) Model

Trainer: CellODE Trainer

cosine_similarity(): Calculate Cosine Similarity

data_utils: Data Utilities for CellODE

extract_expression(): Extract Expression Matrix from Seurat Object

l2_norm(): L2 Norm

load_model(): Load Trained Model

log_nb(): Log Probability of Negative Binomial Distribution

log_zinb(): Log Probability of Zero-Inflated Negative Binomial Distribution

nn_modules: Neural Network Modules for CellODE

normal_kl(): KL Divergence between Two Normal Distributions

ode_solver: Neural ODE Solver for CellODE

odeint(): Forward ODE Integration

plot_loss(): Plot Training Loss

plot_pseudotime(): Plot Pseudotime

plot_vector_field(): Plot Vector Field

plotting: Plotting Functions for CellODE

predict: Prediction Functions for CellODE

predict_latentsp(): Predict Latent Space for Query Cells

predict_ltsp_from_time(): Predict Latent Space from Time Points

predict_time(): Predict Pseudotime for Query Cells

predict_vector_field(): Predict Vector Field for Query Cells

reverse_time(): Reverse Pseudotime

split_data(): Split Data for Training and Validation

split_index(): Split Indices for Training and Validation

train: Training Module for CellODE

utils: Utility Functions for CellODE

vector_field: Vector Field Analysis for CellODE

vector_field_embedding(): Vector Field Embedding

vector_field_embedding_grid(): Vector Field Embedding on Grid

zzz: Package Startup