Metadata-Version: 2.1
Name: omicverse
Version: 1.4.1
Summary: OmicVerse: A single pipeline for exploring the entire transcriptome universe
Home-page: https://github.com/Starlitnightly/omicverse
Author: ZehuaZeng
Author-email: Starlitnightly@163.com
License: GNU License
Platform: UNKNOWN
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE

<h1 align="center">
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</h1><br>

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

The original name of the omicverse was [Pyomic](https://pypi.org/project/Pyomic/), but we wanted to address a whole universe of transcriptomics, so we changed the name to OmicVerse, it aimed to solve all task in RNA-seq.

## Directory structure

````shell
.
├── omicverse                  # Main Python package
├── omicverse_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 omicverse
```

## Usage

Please checkout the documentations and tutorials at [omicverse.readthedocs.io](https://omicverse.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)
- [11] [pyDEseq2](https://github.com/owkin/PyDESeq2) was originally avaliable in [*biorxiv*](https://www.biorxiv.org/content/10.1101/2022.12.14.520412v1)
- [12] [NOCD](https://github.com/shchur/overlapping-community-detection) was originally avaliable in [*Deep Learning on Graphs Workshop, KDD*](https://arxiv.org/abs/1909.12201)

## Contact

- Zehua Zeng ([starlitnightly@163.com](mailto:starlitnightly@163.com) or [zehuazeng@xs.ustb.edu.cn](mailto:zehuazeng@xs.ustb.edu.cn))

## Other

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