A package for analyzing cell type using single-cell RNA-sequencing data.
Project description
scTOP: Single-cell Type Order Parameters
A Python package for analyzing cell type using single-cell RNA-sequencing data. See our paper for more details: Development.
Documentation available via Read the Docs
Please report bugs or request new features in the Github “Issues” tab. You can also contact Maria or Huan directly at mariay@bu.edu and hsouza@bu.edu.
Installation
To install using pip: pip install sctop To install from github: clone or download this repo and import the module from the sctop directory.
Dependencies
NumPy
Pandas
SciPy
scikit-learn
Anndata
tqdm
numba
matplotlib
seaborn
tables
requests
Sources for reference databases
Herriges et al. <https://doi.org/10.1101/2022.07.26.501591>
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