scTour

<img src="https://github.com/LiQian-XC/sctour/blob/main/docs/source/_static/img/scTour_head_image.png" width="400px" align="left">

scTour is an innovative and comprehensive method for dissecting cellular dynamics by analysing datasets derived from single-cell genomics.

It provides a unifying framework to depict the full picture of developmental processes from multiple angles including the developmental pseudotime, vector field and latent space.

It further generalises these functionalities to a multi-task architecture for within-dataset inference and cross-dataset prediction of cellular dynamics in a batch-insensitive manner.

Key features

• cell pseudotime estimation with no need for specifying starting cells.
• transcriptomic vector field inference with no discrimination between spliced and unspliced mRNAs.
• latent space mapping by combining intrinsic transcriptomic structure with extrinsic pseudotime ordering.
• model-based prediction of pseudotime, vector field, and latent space for query cells/datasets/time intervals.
• insensitive to batch effects; robust to cell subsampling; scalable to large datasets.

Installation

consoleCopy
pip install sctour

consoleCopy
conda install -c conda-forge sctour

Documentation

Full documentation can be found here.

Reference

Qian Li, scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics. Genome Biology, 2023