celldancer 1.1.7

Study RNA velocity through neural network.

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.

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 v1.1.7

• 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, 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/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.