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ForwardYang98 authored Jan 8, 2024
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[![python >=3.8](https://img.shields.io/badge/python-%3E%3D3.8-brightgreen)](https://www.python.org/)

scCube is a Python package coupled with an interactive website for reproducible, paired, and platform-diverse simulation of spatially-resolved transcriptomic data
scCube is a Python package for independent, reproducible, and platform-diverse simulation of spatially-resolved transcriptomic data

![avatar](images/workflow.jpg)
## Major updates in v2.0.0
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2. **scCube now allows users to generate more interpretable spatial patterns in a customized manner:**
* [Simulation of biologically interpretable spatial basis patterns](tutorial/customized_basis_patterns.ipynb)
* [Simulation of highly customized complex spatial patterns](tutorial/customized_complex_patterns.ipynb)
* [Demonstration on simulating the tumor-immune microenvironment of TNBC with three archetypical subtypes](tutorial/customized_TME.ipynb)
* [Demonstration on simulating the tumor-immune microenvironment of TNBC with three archetypical subtypes](tutorial/customized_TME.ipynb)

## To-Do list
1. **Other deep generative models (such as CGAN) for gene expression simulation**

## Requirements and Installation
[![anndata 0.8.0](https://img.shields.io/badge/anndata-0.8.0-success)](https://pypi.org/project/anndata/) [![numpy 1.23.5](https://img.shields.io/badge/numpy-1.23.5-important)](https://pypi.org/project/numpy/) [![pandas 1.5.3](https://img.shields.io/badge/pandas-1.5.3-critical)](https://pypi.org/project/pandas/) [![scanpy 1.9.1](https://img.shields.io/badge/scanpy-1.9.1-informational)](https://github.com/scverse/scanpy) [![pot 0.8.2](https://img.shields.io/badge/pot-0.8.2-blueviolet)](https://pypi.org/project/POT/) [![matplotlib 3.6.3](https://img.shields.io/badge/matplotlib-3.6.3-ff69b4)](https://pypi.org/project/matplotlib/) [![seaborn 0.12.2](https://img.shields.io/badge/seaborn-0.12.2-9cf)](https://pypi.org/project/seaborn/) [![tqdm 4.64.1](https://img.shields.io/badge/tqdm-4.64.1-lightgrey)](https://pypi.org/project/tqdm/)
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