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

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# scTour

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

[![PyPI](https://img.shields.io/pypi/v/sctour.svg?color=brightgreen&style=flat)](https://pypi.org/project/sctour)

```console
pip install sctour
```

[![Conda](https://img.shields.io/conda/vn/conda-forge/sctour.svg?color=brightgreen&style=flat)](https://anaconda.org/conda-forge/sctour)

```console
conda install -c conda-forge sctour
```

## Documentation

[![Documentation Status](https://readthedocs.org/projects/sctour/badge/?version=latest)](https://sctour.readthedocs.io/en/latest/?badge=latest)

Full documentation can be found [here](https://sctour.readthedocs.io/en/latest/).

## Reference

[Qian Li, scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics. Genome Biology, 2023](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02988-9)

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