cellDancer - Estimating Cell-dependent RNA Velocity

cellDancer is a modularized, parallelized, and scalable tool based on a deep learning framework for the RNA velocity analysis of scRNA-seq. Our website of tutorials is available at cellDancer Website.

Cite

Shengyu Li#, Pengzhi Zhang#, Weiqing Chen, Lingqun Ye, Kristopher W. Brannan, Nhat-Tu Le, Jun-ichi Abe, John P. Cooke, Guangyu Wang. A relay velocity model infers cell-dependent RNA velocity. Nature Biotechnology (2023) https://doi.org/10.1038/s41587-023-01728-5

cellDancer's key applications

• Estimate cell-specific RNA velocity for each gene.
• Derive cell fates in embedding space.
• Estimate pseudotime for each cell in embedding space.

What's new

cellDancer is updated to v1.1.4

• Our work of cellDancer has been published at Nature Biotechnology!
• Released cellDancer at PyPI. Mainly updated requirements.txt and setup.py.

cellDancer is updated to v1.1.3

• Added celldancer.utilities.to_dynamo and celldancer.utilities.export_velocity_to_dynamo to import cellDancer results to dynamo.
• Added deep learning parameters n_neighbors, dt, and learning_rate in function cellDancer.velocity().
• Added new loss function: mix, rmse in function cellDancer.velocity().

Installation

cellDancer requires Python version >= 3.7.6 to run.

To run cellDancer locally, create an conda or Anaconda environment as conda create -n cellDancer python==3.7.6, and activate the new environment with conda activate cellDancer. cellDancer could be installed with pip install celldancer.

To install cellDancer from source code, run: pip install 'your_path/cellDancer'.

For M1 Mac users if you encountered a problem while installing bezier. Please refer to the following link: https://bezier.readthedocs.io/en/2021.2.12/#installing

If any other dependency could not be installed with pip install celldancer, try pip install --no-deps celldancer. Then install the dependencies by pip install -r requirements.txt or install each package independently..