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