Metadata-Version: 2.1
Name: cell-bin
Version: 1.2.6
Summary: A framework for generating single-cell gene expression data
Home-page: https://gitlab.genomics.cn/biointelligence/implab/stero-rnd/cellbin/algorithms/cellbin/-/tree/dev
Author: cell bin research group
Author-email: bgi@genomics.cn
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Requires-Python: ==3.8.*
Description-Content-Type: text/markdown
Requires-Dist: numpy (>=1.22.3)
Requires-Dist: tifffile (>=2023.2.3)
Requires-Dist: scikit-image (>=0.21.0)
Requires-Dist: opencv-python (>=4.8.0.76)
Requires-Dist: onnxruntime (>=1.15.1)
Requires-Dist: tqdm (>=4.65.0)
Requires-Dist: scikit-learn (>=1.3.0)
Requires-Dist: imagecodecs (>=2023.3.16)
Requires-Dist: pandas (>=1.5.3)
Requires-Dist: matplotlib (>=3.7.1)
Requires-Dist: pyvips (>=2.2.1)

<div align="center">
  <img src="docs/images/cellbin.png"><br/>
  <h4 align="center">
    A framework for generating single-cell gene expression data
  </h4>
</div>

# WHL
If you just want to use this repo, you may download whl, install it using pip. (very fast)

**cellbin-0.7.0 whl and later will move to the drive below**

BGI new cloud

- Have shared link to product, develop and research
- If you do not have permission, please ask **dengzhonghan@genoimics.cn**


cellbin-0.6.2 and older whl, please see below link

[BGI cloud](https://pan.genomics.cn/ucdisk/s/iMzyMn)


[Version notes](docs/version.md)


# Installation
Both on Windows or Linux (CentOS, Ubuntu), just
```shell
pip install -r requirements.txt
```

Pyvips linux installation
```shell
# linux environ install pyvips using conda
conda install --channel conda-forge pyvips
```

Pyvips windows install vips from [vips](https://github.com/libvips/libvips/releases)
```shell
pip install --user pyvips==2.2.1
```

```python
# add vips path when running python script
import os
vipsbin = r'c:\vips-dev-8.13\bin'
os.environ['PATH'] = vipsbin + ';' + os.environ['PATH']
```

# Develop mode
```shell
git clone https://gitlab.genomics.cn/biointelligence/implab/stero-rnd/cellbin/algorithms/cellbin.git
conda activate env # activate your env
python setup.py develop --no-deps  # develop mode, if you already have deps installed
```

# Usage
* API doc
* [How to get weights?](docs/weights.md)


## <div align="center">contribute</div>
We love your input! We want to make contributing to cellbin as easy and transparent as possible. Please see,
- When you need to change other people's modules, remember to note the change information in the change location. like,
``` a = 0  #  parameter value to zero [by jack]```
- 
Thank you to all our contributors!

## <div align="center">Cellbin HUB</div>

* [ImageQC-Research](https://gitlab.genomics.cn/biointelligence/implab/stero-rnd/cellbin/tools/pipeline-research.git)
* [Pipeline-Research](https://gitlab.genomics.cn/biointelligence/implab/stero-rnd/cellbin/tools/pipeline-research.git)

## <div align="center">Contact</div>

For cellbin bugs and feature requests please visit 
