API
Import dynamo as:
import dynamo as dyn
Data IO
(See more at anndata-docs)
Preprocessing (pp)
Estimation (est)
Note
Classes in est are internally to Tools. See our estimation classes here: estimation
Tools (tl)
kNN and moments of expressions
Kinetic parameters and RNA/protein velocity
Dimension reduction
Clustering
Velocity projection
Velocity metrics
Markov chain
Markers and differential expressions
Cell proliferation and apoptosis
Converter
Vector field (vf)
Vector field reconstruction
Note
Vector field class is internally to vf.VectorField. See our vector field classes here: vector field
Vector field topology
Beyond RNA velocity
Beyond velocity vector field
Vector field ranking
Single cell potential: three approaches
Stochastic processes
Vector field graph
Prediction (pd)
Plotting (pl)
Preprocessing
Cell cycle staging
Scatter base
Phase diagram: conventional scRNA-seq
Kinetic models: labeling based scRNA-seq
Kinetics
Dimension reduction
Neighbor graph
Vector field plots: velocities and accelerations
Vector field topology
Beyond RNA velocity
Potential landscape
Cell fate
Save figures
Moive (mv)
Note
animation class is internally to mv.animate_fates. See our animation classes here: animation
Simulation (sim)
Simple ODE vector field simulation
Gillespie simulation
External (ext)
Utilities
Package versions
Clean up adata
Figures configuration