Metadata-Version: 2.1
Name: Pyomic
Version: 1.2.9
Summary: A python framework library for omics analysis
Home-page: https://github.com/Starlitnightly/Pyomic
Author: ZehuaZeng
Author-email: Starlitnightly@163.com
License: GNU License
Platform: UNKNOWN
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pybind11
Requires-Dist: hnswlib
Requires-Dist: ERgene
Requires-Dist: numpy
Requires-Dist: scanpy
Requires-Dist: pandas (==1.5.3)
Requires-Dist: matplotlib
Requires-Dist: scikit-learn
Requires-Dist: scipy
Requires-Dist: networkx
Requires-Dist: multiprocess
Requires-Dist: seaborn
Requires-Dist: datetime
Requires-Dist: statsmodels
Requires-Dist: gseapy (==0.10.8)
Requires-Dist: ipywidgets
Requires-Dist: lifelines
Requires-Dist: ktplotspy
Requires-Dist: python-dotplot
Requires-Dist: boltons
Requires-Dist: ctxcore
Requires-Dist: termcolor
Requires-Dist: pygam (==0.8.0)
Requires-Dist: pillow
Requires-Dist: gdown
Requires-Dist: igraph
Requires-Dist: leidenalg
Requires-Dist: s-gd2
Requires-Dist: graphtools
Requires-Dist: datashader
Requires-Dist: phate
Requires-Dist: wget

<h1 align="center">
<img src="https://raw.githubusercontent.com/Starlitnightly/Pyomic/master/README.assets/logo.svg" width="400">
</h1><br>

[![Lifecycle:maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) [![bulid:passing](https://img.shields.io/appveyor/build/gruntjs/grunt)](https://img.shields.io/appveyor/build/gruntjs/grunt) [![License:GPL](https://img.shields.io/badge/license-GNU-blue)](https://img.shields.io/apm/l/vim-mode) [![pypi-badge](https://img.shields.io/pypi/v/Pyomic)](https://pypi.org/project/Pyomic) [![Documentation Status](https://readthedocs.org/projects/pyomic/badge/?version=latest)](https://pyomic.readthedocs.io/en/latest/?badge=latest) 

Pyomic is the fundamental package for multi omics included bulk and single cell analysis with Python.

## Directory structure

````shell
.
├── Pyomic                  # Main Python package
├── pyomic_guide            # Documentation files
├── sample                  # Some test data
├── LICENSE
└── README.md
````

## Where to get it

Binary installers for the latest released version are available at the pypi

```shell
pip install -U Pyomic
```

## Usage

Please checkout the documentations and tutorials at [pyomic.readthedocs.io](https://pyomic.readthedocs.io/en/latest/index.html).

## Reference

- [1] [dynamicTreeCut](https://github.com/kylessmith/dynamicTreeCut) was originally published by in [*Bioinformatics*](https://academic.oup.com/bioinformatics/article/24/5/719/200751) 
- [2] [scDrug](https://github.com/ailabstw/scDrug) was originally published in [*Computational and Structural Biotechnology Journal*](https://www.sciencedirect.com/science/article/pii/S2001037022005505)
- [3] [MOFA](https://github.com/bioFAM/mofapy2) was originally published in [*Genome Biology*](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02015-1)
- [4] [COSG](https://github.com/genecell/COSG) was originally published in [*Briefings in Bioinformatics*](https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab579/6511197?redirectedFrom=fulltext)
- [5] [CellphoneDB](https://github.com/ventolab/CellphoneDB) was originally published in [*Nature*](https://www.nature.com/articles/s41586-018-0698-6)
- [6] [AUCell](https://github.com/aertslab/AUCell) was originally available in [*Bioconductor*](https://bioconductor.org/packages/AUCell), and we use the script of Pyscenic to instead.
- [7] [Bulk2Space](https://github.com/ZJUFanLab/bulk2space) was originally available in [*Nature Communications*](https://www.nature.com/articles/s41467-022-34271-z)
- [8] [SCSA](https://github.com/bioinfo-ibms-pumc/SCSA) was originally availabale in [*Front Genet*](https://doi.org/10.3389/fgene.2020.00490)
- [9] [WGCNA](http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA) was originally avaliable in [*BMC Bioinformatics*](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-559)
- [10] [VIA](https://github.com/ShobiStassen/VIA) was originally avaliable in [*Nature Communications*](https://www.nature.com/articles/s41467-021-25773-3)

## Contact

- Zehua Zeng ([starlitnightly@163.com](mailto:starlitnightly@163.com))

## Other

<div>Logo made by <a href="https://www.designevo.com/" title="Free Online Logo Maker">DesignEvo free logo creator</a></div>



