cellDancer
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Predict RNA velocity through deep learning
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 [email protected]
Support
Welcome bug reports and suggestions to our GitHub issue page!