Pseudotime Python Packages

scfates

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

scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

sctour

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

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

scarf-toolkit

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.