Trajectory Inference Python Packages

pyvia

trajectory inference

pyvitae

Joint Trajectory Inference for Single-cell Genomics Using Deep Learning with a Mixture Prior

genomap

Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)

bioiot

Plug-and-play semi-relaxed inverse optimal transport (IOT) in Python: Anderson-accelerated soft Sinkhorn with exact implicit gradients, sklearn-style fitting, transition matrices, random-walk pseudotime, AnnData/scanpy interface, matplotlib plots. numpy in, numpy out.

cytopath

Simulation based inference of differentiation trajectories from RNA velocity fields.

phlowerpy

Use hodge decomposition for trajectory analysis