Pseudotime Python Packages

scfates

a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.

sctour

A deep learning architecture for robust inference and accurate prediction of cellular dynamics

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.

scltnn

A composite regression neural network for latent timing prediction of single-cell RNA-seq data

sceptic

Pseudotime analysis for time-series single-cell sequencing and imaging data