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 <https://guangyuwanglab2021.github.io/cellDancer_website/>_.

.. image:: _static/training_progress.png :width: 100% :alt: cell_type_u_s_sample_df

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

• Enable accurate inference of dynamic cell state transitions in heterogeneous cell populations.
• Estimate cell-specific transcription (α), splicing (β) and degradation (γ) rates for each gene and reveal RNA turnover strategies.
• Improves downstream analysis such as vector field predictions.

To be done

• [ ] Update an anndata-compatible version.

What's new

cellDancer is updated to v1.1.7

• Added progress bar for adata_to_df_with_embed() and adata_to_raw().
• Added try except to catch genes with low quality in velocity().

Installation

cellDancer requires Python version >= 3.7.6 to run.

To run cellDancer locally, we recommend to create a conda <https://docs.conda.io/en/latest>_ environment: conda create -n cellDancer python==3.7.6. Then activate the new environment with conda activate cellDancer. cellDancer package could be installed from pypi with pip install celldancer.

Python 3.7 is not compatible with M1 Mac, conda create -n cellDancer python==3.9.16 is the version that compatible with M1 Mac that has been well tested to run cellDancer.

To install the latest version from GitHub, run:

pip install git+https://github.com/GuangyuWangLab2021/cellDancer.git

To install cellDancer from source code, run:

pip install 'your_path/Source Code/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 manually install each package in requirements.txt.

To be compatible with Dynamo (optional), after first pip install celldancer and then pip install dynamo-release, installing Dynamo will update numpy to 1.24.0, and we can downgrade numpy back to 1.20.0 with pip install numpy==1.20.0 to let them be compatible.

Frequently asked questions

Q: How should I prepare the input for my own data?

A: The Data Preparation <https://guangyuwanglab2021.github.io/cellDancer_website/data_preprocessing.html>_ page introduces the details of how to prepare and pre-process your own data.

Check more frequently asked questions at FAQ <https://guangyuwanglab2021.github.io/cellDancer_website/FAQ.html> in our website. If you have any other question related to your specific contition, welcome to post it in our github issue <https://github.com/GuangyuWangLab2021/cellDancer/issues> page or email to sli5@houstonmethodist.org

Support

Welcome bug reports and suggestions to our GitHub issue page!