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[![pypi-badge](https://img.shields.io/pypi/v/omicverse)](https://pypi.org/project/omicverse) [![Documentation Status](https://readthedocs.org/projects/omicverse/badge/?version=latest)](https://omicverse.readthedocs.io/en/latest/?badge=latest) [![pypiDownloads](https://static.pepy.tech/badge/omicverse)](https://pepy.tech/project/omicverse) [![condaDownloads](https://img.shields.io/conda/dn/conda-forge/omicverse?logo=Anaconda)](https://anaconda.org/conda-forge/omicverse) [![License:GPL](https://img.shields.io/badge/license-GNU-blue)](https://img.shields.io/apm/l/vim-mode) [![scverse](https://img.shields.io/badge/scverse-ecosystem-blue.svg?labelColor=yellow)](https://scverse.org/) [![Pytest](https://github.com/Starlitnightly/omicverse/workflows/py38|py39/badge.svg)](https://github.com/Starlitnightly/omicverse/) | ||
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OmicVerse is the fundamental package for multi omics included bulk ,single cell and spatial RNA-seq analysis with Python. For more information, please read our paper: [OmicVerse: A single pipeline for exploring the entire transcriptome universe](https://www.biorxiv.org/content/10.1101/2023.06.06.543913v2) | ||
**`OmicVerse`** is the fundamental package for multi omics included **bulk ,single cell and spatial RNA-seq** analysis with Python. For more information, please read our paper: [OmicVerse: A single pipeline for exploring the entire transcriptome universe](https://www.biorxiv.org/content/10.1101/2023.06.06.543913v2) | ||
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> \[!IMPORTANT] | ||
> [!IMPORTANT] | ||
> | ||
> **Star Us**, You will receive all release notifications from GitHub without any delay \~ ⭐️ | ||
> \[!NOTE] | ||
> | ||
> If you like **OmicVerse** and want to support our mission, please consider making a [donation](https://afdian.net/a/starlitnightly) to support our efforts. | ||
> If you like **OmicVerse** and want to support our mission, please consider making a [💗donation](https://afdian.net/a/starlitnightly) to support our efforts. | ||
<details> | ||
<summary><kbd>Star History</kbd></summary> | ||
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## `1` [Introduction][docs-feat-provider] | ||
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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. | ||
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. | ||
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BulkTrajBlend algorithm in OmicVerse that combines Beta-Variational AutoEncoder for deconvolution and graph neural networks for overlapping community discovery to effectively interpolate and restore the continuity of “interrupted” cells in the original scRNA-seq data. | ||
> [!NOTE] | ||
> **BulkTrajBlend** algorithm in OmicVerse that combines Beta-Variational AutoEncoder for deconvolution and graph neural networks for overlapping community discovery to effectively interpolate and restore the continuity of **"omission"** cells in the original scRNA-seq data. | ||
![omicverse-light](omicverse_guide/docs/img/omicverse.png#gh-light-mode-only) | ||
![omicverse-dark](omicverse_guide/docs/img/omicverse_dark.png#gh-dark-mode-only) | ||
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- Zehua Zeng ([[email protected]](mailto:[email protected]) or [[email protected]](mailto:[email protected])) | ||
- Lei Hu ([[email protected]](mailto:[email protected])) | ||
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## `6` [Developer Guild and Acknowledgements](#) | ||
## `6` [Developer Guild and Contributing](#) | ||
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If you would like to contribute to omicverse, please refer to our [developer documentation](https://omicverse.readthedocs.io/en/latest/Developer_guild/). | ||
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<table align="center"> | ||
<tr> | ||
<th colspan="2"> | ||
<br><img src="https://contrib.rocks/image?repo=Starlitnightly/omicverse"><br><br> | ||
</th> | ||
</tr> | ||
</table> | ||
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> [!IMPORTANT] | ||
> We would like to thank the following WeChat Official Accounts for promoting Omicverse. | ||
> <p align="center"> <a href="http://www.biotrainee.com/" target="_blank" rel="noreferrer"> <img src="README.assets/image-20230701163953794.png" alt="linux" width="50" height="50"/> </a> <a href="https://zhuanlan.zhihu.com/c_1257815636945915904?page=3" target="_blank" rel="noreferrer"> <img src="README.assets/WechatIMG688.png" alt="linux" width="50" height="50"/> </a> </p> | ||
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<p align="center"> <a href="http://www.biotrainee.com/" target="_blank" rel="noreferrer"> <img src="README.assets/image-20230701163953794.png" alt="linux" width="50" height="50"/> </a> <a href="https://zhuanlan.zhihu.com/c_1257815636945915904?page=3" target="_blank" rel="noreferrer"> <img src="README.assets/WechatIMG688.png" alt="linux" width="50" height="50"/> </a> </p> | ||
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## `7` [Other](#) | ||
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