Metadata-Version: 2.1
Name: celldancer
Version: 1.1.7
Summary: Study RNA velocity through neural network.
Author: Wang Lab
Author-email: gwang2@houstonmethodist.org
Project-URL: cellDancer, https://github.com/GuangyuWangLab2021/cellDancer
Project-URL: Documentation, https://guangyuwanglab2021.github.io/cellDancer_website/
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7.6
Description-Content-Type: text/x-rst; charset=UTF-8
License-File: LICENSE
Requires-Dist: pytorch-lightning (==1.5.2)
Requires-Dist: torch (==1.10.0)
Requires-Dist: pandas (==1.3.4)
Requires-Dist: numpy (==1.20.3)
Requires-Dist: anndata (==0.8.0)
Requires-Dist: tqdm (==4.62.3)
Requires-Dist: scikit-learn (==1.0.1)
Requires-Dist: scipy (==1.7.2)
Requires-Dist: joblib (==1.1.0)
Requires-Dist: scikit-image (==0.19.2)
Requires-Dist: statsmodels (==0.13.1)
Requires-Dist: matplotlib (==3.5.3)
Requires-Dist: seaborn (==0.11.2)
Requires-Dist: datashader (==0.14.0)
Requires-Dist: bezier (==2021.2.12)
Requires-Dist: umap-learn (==0.5.2)
Requires-Dist: jupyterlab
Requires-Dist: setuptools (==59.5.0)
Requires-Dist: setuptools-scm (==6.3.2)

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/>`_.


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 <https://docs.conda.io/en/latest>`_ or `Anaconda <https://www.anaconda.com/>`_ 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``.
