omicverse 1.7.8
OmicVerse: A single pipeline for exploring the entire transcriptome universe
Requires Python: >=3.8
Keywords: bioinformatics, deep-learning, scRNA-seq, RNA-seq

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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 framework for bridging and deepening insights across bulk and single-cell sequencing](https://www.nature.com/articles/s41467-024-50194-3)

> [!IMPORTANT]
>
> **Star Us**, You will receive all release notifications from GitHub without any delay \~ ⭐️
>
> If you like **OmicVerse** and want to support our mission, please consider making a [💗donation](https://ifdian.net/a/starlitnightly) to support our efforts.

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## `1` [Introduction][docs-feat-provider]

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.

> [!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)


## `2` [Directory structure](#)

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

## `3` [Getting Started ](#)

OmicVerse can be installed via conda or pypi and you need to install `pytorch` at first. Please refer to the [installation tutorial](https://starlitnightly.github.io/omicverse/Installation_guild/) for more detailed installation steps and adaptations for different platforms (`Windows`, `Linux` or `Mac OS`).

You can use `conda install omicverse -c conda-forge` or `pip install -U omicverse` for installation.

Please checkout the documentations and tutorials at [omicverse page](https://starlitnightly.github.io/omicverse/) or [omicverse.readthedocs.io](https://omicverse.readthedocs.io/en/latest/index.html).


## `4` [Data Framework and Reference](#)

The omicverse is implemented as an infrastructure based on the following four data structures.

<div align="center">
<table>
  <tr>
    <td> <a href="https://github.com/pandas-dev/pandas">pandas</a></td>
    <td> <a href="https://github.com/scverse/anndata">anndata</a></td>
    <td> <a href="https://github.com/numpy/numpy">numpy</a></td>
    <td> <a href="https://github.com/scverse/mudata">mudata</a></td>
  </tr>

</table>
</div>

---

The table contains the tools have been published 

<div align="center">
<table>

  <tr>
    <td align="center">Scanpy<br><a href="https://github.com/scverse/scanpy">📦</a> <a href="https://link.springer.com/article/10.1186/s13059-017-1382-0">📖</a></td>
    <td align="center">dynamicTreeCut<br><a href="https://github.com/kylessmith/dynamicTreeCut">📦</a> <a href="https://academic.oup.com/bioinformatics/article/24/5/719/200751">📖</a></td>
    <td align="center">scDrug<br><a href="https://github.com/ailabstw/scDrug">📦</a> <a href="https://www.sciencedirect.com/science/article/pii/S2001037022005505">📖</a></td>
    <td align="center">MOFA<br><a href="https://github.com/bioFAM/mofapy2">📦</a> <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02015-1">📖</a></td>
    <td align="center">COSG<br><a href="https://github.com/genecell/COSG">📦</a> <a href="https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab579/6511197?redirectedFrom=fulltext">📖</a></td>
    <td align="center">CellphoneDB<br><a href="https://github.com/ventolab/CellphoneDB">📦</a> <a href="https://www.nature.com/articles/s41586-018-0698-6">📖</a></td>
    </tr>

  <tr>
    <td align="center">AUCell<br><a href="https://github.com/aertslab/AUCell">📦</a> <a href="https://bioconductor.org/packages/AUCell">📖</a></td>
    <td align="center">Bulk2Space<br><a href="https://github.com/ZJUFanLab/bulk2space">📦</a> <a href="https://www.nature.com/articles/s41467-022-34271-z">📖</a></td>
    <td align="center">SCSA<br><a href="https://github.com/bioinfo-ibms-pumc/SCSA">📦</a> <a href="https://doi.org/10.3389/fgene.2020.00490">📖</a></td>
    <td align="center">WGCNA<br><a href="http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA">📦</a> <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-559">📖</a></td>
    <td align="center">StaVIA<br><a href="https://github.com/ShobiStassen/VIA">📦</a> <a href="https://www.nature.com/articles/s41467-021-25773-3">📖</a></td>
    <td align="center">pyDEseq2<br><a href="https://github.com/owkin/PyDESeq2">📦</a> <a href="https://www.biorxiv.org/content/10.1101/2022.12.14.520412v1">📖</a></td>
</tr>

  <tr>
    <td align="center">NOCD<br><a href="https://github.com/shchur/overlapping-community-detection">📦</a> <a href="https://arxiv.org/abs/1909.12201">📖</a></td>
    <td align="center">SIMBA<br><a href="https://github.com/pinellolab/simba">📦</a> <a href="https://www.nature.com/articles/s41592-023-01899-8">📖</a></td>
    <td align="center">GLUE<br><a href="https://github.com/gao-lab/GLUE">📦</a> <a href="https://www.nature.com/articles/s41587-022-01284-4">📖</a></td>
    <td align="center">MetaTiME<br><a href="https://github.com/yi-zhang/MetaTiME">📦</a> <a href="https://www.nature.com/articles/s41467-023-38333-8">📖</a></td>
    <td align="center">TOSICA<br><a href="https://github.com/JackieHanLab/TOSICA">📦</a> <a href="https://doi.org/10.1038/s41467-023-35923-4">📖</a></td>
    <td align="center">Harmony<br><a href="https://github.com/slowkow/harmonypy/">📦</a> <a href="https://www.nature.com/articles/s41592-019-0619-0">📖</a></td>
  </tr>

  <tr>
    <td align="center">Scanorama<br><a href="https://github.com/brianhie/scanorama">📦</a> <a href="https://www.nature.com/articles/s41587-019-0113-3">📖</a></td>
    <td align="center">Combat<br><a href="https://github.com/epigenelabs/pyComBat/">📦</a> <a href="https://doi.org/10.1101/2020.03.17.995431">📖</a></td>
    <td align="center">TAPE<br><a href="https://github.com/poseidonchan/TAPE">📦</a> <a href="https://doi.org/10.1038/s41467-022-34550-9">📖</a></td>
    <td align="center">SEACells<br><a href="https://github.com/dpeerlab/SEACells">📦</a> <a href="https://www.nature.com/articles/s41587-023-01716-9">📖</a></td>
    <td align="center">Palantir<br><a href="https://github.com/dpeerlab/Palantir">📦</a> <a href="https://doi.org/10.1038/s41587-019-0068-49">📖</a></td>
    <td align="center">STAGATE<br><a href="https://github.com/QIFEIDKN/STAGATE_pyG">📦</a> <a href="https://www.nature.com/articles/s41467-022-29439-6">📖</a></td>
  </tr>

  <tr>
    <td align="center">scVI<br><a href="https://github.com/scverse/scvi-tools">📦</a> <a href="https://doi.org/10.1038/s41587-021-01206-w">📖</a></td>
    <td align="center">MIRA<br><a href="https://github.com/cistrome/MIRA">📦</a> <a href="https://www.nature.com/articles/s41592-022-01595-z">📖</a></td>
    <td align="center">Tangram<br><a href="https://github.com/broadinstitute/Tangram/">📦</a> <a href="https://www.nature.com/articles/s41592-021-01264-7">📖</a></td>
    <td align="center">STAligner<br><a href="https://github.com/zhoux85/STAligner">📦</a> <a href="https://doi.org/10.1038/s43588-023-00528-w">📖</a></td>
    <td align="center">CEFCON<br><a href="https://github.com/WPZgithub/CEFCON">📦</a> <a href="https://www.nature.com/articles/s41467-023-44103-3">📖</a></td>
    <td align="center">PyComplexHeatmap<br><a href="https://github.com/DingWB/PyComplexHeatmap">📦</a> <a href="https://doi.org/10.1002/imt2.115">📖</a></td>
      </tr>

  <tr>
    <td align="center">STT<br><a href="https://github.com/cliffzhou92/STT/">📦</a> <a href="https://www.nature.com/articles/s41592-024-02266-x#Sec2">📖</a></td>
    <td align="center">SLAT<br><a href="https://github.com/gao-lab/SLAT">📦</a> <a href="https://www.nature.com/articles/s41467-023-43105-5">📖</a></td>
    <td align="center">GPTCelltype<br><a href="https://github.com/Winnie09/GPTCelltype">📦</a> <a href="https://www.nature.com/articles/s41592-024-02235-4">📖</a></td>
    <td align="center">PROST<br><a href="https://github.com/Tang-Lab-super/PROST">📦</a> <a href="https://doi.org/10.1038/s41467-024-44835-w">📖</a></td>
    <td align="center">CytoTrace2<br><a href="https://github.com/digitalcytometry/cytotrace2">📦</a> <a href="https://doi.org/10.1101/2024.03.19.585637">📖</a></td>
    <td align="center">GraphST<br><a href="https://github.com/JinmiaoChenLab/GraphST">📦</a> <a href="https://www.nature.com/articles/s41467-023-36796-3#citeas">📖</a></td>
  </tr>

  <tr>
    <td align="center">COMPOSITE<br><a href="https://github.com/CHPGenetics/COMPOSITE/">📦</a> <a href="https://www.nature.com/articles/s41467-024-49448-x#Abs1">📖</a></td>
    <td align="center">mellon<br><a href="https://github.com/settylab/mellon">📦</a> <a href="https://www.nature.com/articles/s41592-024-02302-w">📖</a></td>
    <td align="center">starfysh<br><a href="https://github.com/azizilab/starfysh">📦</a> <a href="http://dx.doi.org/10.1038/s41587-024-02173-8">📖</a></td>
    <td align="center">COMMOT<br><a href="https://github.com/zcang/COMMOT">📦</a> <a href="https://www.nature.com/articles/s41592-022-01728-4">📖</a></td>
    <td align="center">flowsig<br><a href="https://github.com/axelalmet/flowsig">📦</a> <a href="https://doi.org/10.1038/s41592-024-02380-w">📖</a></td>
    <td align="center">pyWGCNA<br><a href="https://github.com/mortazavilab/PyWGCNA">📦</a> <a href="https://doi.org/10.1093/bioinformatics/btad415">📖</a></td>
  </tr>

  <tr>
    <td align="center">CAST<br><a href="https://github.com/wanglab-broad/CAST">📦</a> <a href="https://www.nature.com/articles/s41592-024-02410-7">📖</a></td>
    <td align="center">scMulan<br><a href="https://github.com/SuperBianC/scMulan">📦</a> <a href="https://link.springer.com/chapter/10.1007/978-1-0716-3989-4_57">📖</a></td>
    <td align="center">cellANOVA<br><a href="https://github.com/Janezjz/cellanova">📦</a> <a href="https://www.nature.com/articles/s41587-024-02463-1">📖</a></td>
    <td align="center">BINARY<br><a href="https://github.com/senlin-lin/BINARY/">📦</a> <a href="https://www.sciencedirect.com/science/article/pii/S2666979X24001319">📖</a></td>
    <td align="center">GASTON<br><a href="https://github.com/raphael-group/GASTON">📦</a> <a href="https://www.nature.com/articles/s41592-024-02503-3">📖</a></td>
    <td align="center">pertpy<br><a href="https://github.com/scverse/pertpy">📦</a> <a href="https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516">📖</a></td>
  </tr>

  <tr>
    <td align="center">inmoose<br><a href="https://github.com/epigenelabs/inmoose">📦</a> <a href="https://www.nature.com/articles/s41598-025-03376-y">📖</a></td>
    <td align="center">memento<br><a href="https://github.com/yelabucsf/scrna-parameter-estimation">📦</a> <a href="https://www.cell.com/cell/fulltext/S0092-8674(24)01144-9">📖</a></td>
    <td align="center">GSEApy<br><a href="https://github.com/zqfang/GSEApy">📦</a> <a href="https://academic.oup.com/bioinformatics/article-abstract/39/1/btac757/6847088">📖</a></td>
    <td align="center">marsilea<br><a href="https://github.com/Marsilea-viz/marsilea/">📦</a> <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03469-3">📖</a></td>
    <td align="center">scICE<br><a href="https://github.com/Mathbiomed/scICE">📦</a> <a href="https://www.nature.com/articles/s41467-025-60702-8">📖</a></td>
    <td align="center">sude<br><a href="https://github.com/ZPGuiGroupWhu/sude">📦</a> <a href="https://www.nature.com/articles/s42256-025-01112-9">📖</a></td>
  </tr>

  <tr>
    <td align="center">GeneFromer<br><a href="https://huggingface.co/ctheodoris/Geneformer">📦</a> <a href="https://www.nature.com/articles/s41586-023-06139-9">📖</a></td>
    <td align="center">scGPT<br><a href="https://github.com/bowang-lab/scGPT">📦</a> <a href="https://www.nature.com/articles/s41592-024-02201-0">📖</a></td>
    <td align="center">scFoundation<br><a href="https://github.com/biomap-research/scFoundation">📦</a> <a href="https://www.nature.com/articles/s41592-024-02305-7">📖</a></td>
    <td align="center">UCE<br><a href="https://github.com/snap-stanford/UCE">📦</a> <a href="https://www.biorxiv.org/content/10.1101/2023.11.28.568918v1.full.pdf">📖</a></td>
    <td align="center">CellPLM<br><a href="https://github.com/OmicsML/CellPLM">📦</a> <a href="https://www.biorxiv.org/content/10.1101/2023.10.03.560734v1">📖</a></td>
    <td align="center">kb_python<br><a href="https://github.com/pachterlab/kb_python">📦</a> <a href="https://doi.org/10.1038/s41596-024-01057-0">📖</a></td>

  </tr>

  <tr>
    <td align="center">Scaden<br><a href="https://github.com/KevinMenden/scaden">📦</a> <a href="https://www.science.org/doi/10.1126/sciadv.aba2619">📖</a></td>
    <td align="center">BayesPrime<br><a href="https://github.com/Danko-Lab/BayesPrism">📦</a> <a href="https://github.com/ziluwang829/pyBayesPrism">📦</a> <a href="https://www.nature.com/articles/s43018-022-00356-3">📖</a></td>
    <td align="center">InstaPrime<br><a href="https://github.com/humengying0907/InstaPrism">📦</a> <a href="https://academic.oup.com/bioinformatics/article/40/7/btae440/7708397">📖</a></td>


  </tr>
</table>
</div>

---

**Included Package not published or preprint**

- [1] [Cellula](https://github.com/andrecossa5/Cellula/) is to provide a toolkit for the exploration of scRNA-seq. These tools perform common single-cell analysis tasks
- [2] [pegasus](https://github.com/lilab-bcb/pegasus/) is a tool for analyzing transcriptomes of millions of single cells. It is a command line tool, a python package and a base for Cloud-based analysis workflows.
- [3] [cNMF](https://github.com/dylkot/cNMF) is an analysis pipeline for inferring gene expression programs from single-cell RNA-Seq (scRNA-Seq) data.

## `5` [Contact](#)

- Zehua Zeng ([starlitnightly@gmail.com](mailto:starlitnightly@gmail.com) or [zehuazeng@xs.ustb.edu.cn](mailto:zehuazeng@xs.ustb.edu.cn))
- Lei Hu ([hulei@westlake.edu.cn](mailto:hulei@westlake.edu.cn))

## `6` [Developer Guild and Contributing](#)

If you would like to contribute to omicverse, please refer to our [developer documentation](https://omicverse.readthedocs.io/en/latest/Developer_guild/).

<table align="center">
    <tr>
      <th colspan="2">
        <br><img src="https://contrib.rocks/image?repo=Starlitnightly/omicverse"><br><br>
      </th>
    </tr>
</table>


> [!IMPORTANT]  
> We would like to thank the following WeChat Official Accounts for promoting Omicverse.
> <p align="center"> <a href="https://mp.weixin.qq.com/s/egAnRfr3etccU_RsN-zIlg" 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>


## `7` [Citation](https://doi.org/10.1038/s41467-024-50194-3)

If you use `omicverse` in your work, please cite the `omicverse` publication as follows:

> **OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing**
>
> Zeng, Z., Ma, Y., Hu, L. et al.
>
> _Nature Communication_ 2024 Jul 16. doi: [10.1038/s41467-024-50194-3](https://doi.org/10.1038/s41467-024-50194-3).

Here are some other related packages, feel free to reference them if you use them!

> **CellOntologyMapper: Consensus mapping of cell type annotation**
>
> Zeng, Z., Wang, X., Du, H.
>
> _bioRxiv_ 2025 Jun 20. doi: [10.1101/2025.06.10.658951](https://doi.org/10.1101/2025.06.10.658951).


## `8` [Other](#)

If you would like to sponsor the development of our project, you can go to the afdian website (https://ifdian.net/a/starlitnightly) and sponsor us.


Copyright © 2024 [112 Lab](https://112lab.asia/). <br />
This project is [GPL3.0](./LICENSE) licensed.

<!-- LINK GROUP -->
[docs-feat-provider]: https://starlitnightly.github.io/omicverse/