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| [](https://pypi.org/project/omicverse) [](https://omicverse.readthedocs.io/en/latest/?badge=latest) [](https://pepy.tech/project/omicverse) [](https://anaconda.org/conda-forge/omicverse) [](https://img.shields.io/apm/l/vim-mode) [](https://scverse.org/) [](https://github.com/Starlitnightly/omicverse/) | ||
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| OmicVerse is the fundamental package for multi omics included bulk and single cell 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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| If you like **OmicVerse** and want to support our mission, please consider making a [donation](https://afdian.net/a/starlitnightly) to support our efforts. | ||
| > \[!IMPORTANT] | ||
| > | ||
| > **Star Us**, You will receive all release notifications from GitHub without any delay \~ ⭐️ | ||
| ## Introduction | ||
| > \[!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. | ||
| <details> | ||
| <summary><kbd>Star History</kbd></summary> | ||
| <picture> | ||
| <source media="(prefers-color-scheme: dark)" srcset="https://api.star-history.com/svg?repos=Starlitnightly%2Fomicverse&theme=dark&type=Date"> | ||
| <img width="100%" src="https://api.star-history.com/svg?repos=Starlitnightly%2Fomicverse&type=Date"> | ||
| </picture> | ||
| </details> | ||
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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. | ||
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| ## Directory structure | ||
| ## `2` [Directory structure](#) | ||
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| ````shell | ||
| . | ||
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| └── README.md | ||
| ```` | ||
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| ## Where to get it | ||
| ## `3` [Getting Started ](#) | ||
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| 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`). | ||
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| You can use `conda install omicverse -c conda-forge` or `pip install -U omicverse` for installation. | ||
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| ## Usage | ||
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| 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). | ||
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| ## Data Framework | ||
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| - [pandas](https://github.com/pandas-dev/pandas) | ||
| - [anndata](https://github.com/scverse/anndata) | ||
| - [numpy](https://github.com/numpy/numpy) | ||
| - [mudata](https://github.com/scverse/mudata) | ||
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| ## Reference | ||
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| - [1] [Scanpy](https://github.com/scverse/scanpy) was originally published in [*Genome biology*](https://link.springer.com/article/10.1186/s13059-017-1382-0) | ||
| - [2] [dynamicTreeCut](https://github.com/kylessmith/dynamicTreeCut) was originally published in [*Bioinformatics*](https://academic.oup.com/bioinformatics/article/24/5/719/200751) | ||
| - [3] [scDrug](https://github.com/ailabstw/scDrug) was originally published in [*Computational and Structural Biotechnology Journal*](https://www.sciencedirect.com/science/article/pii/S2001037022005505) | ||
| - [4] [MOFA](https://github.com/bioFAM/mofapy2) was originally published in [*Genome Biology*](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02015-1) | ||
| - [5] [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) | ||
| - [6] [CellphoneDB](https://github.com/ventolab/CellphoneDB) was originally published in [*Nature*](https://www.nature.com/articles/s41586-018-0698-6) | ||
| - [7] [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. | ||
| - [8] [Bulk2Space](https://github.com/ZJUFanLab/bulk2space) was originally published in [*Nature Communications*](https://www.nature.com/articles/s41467-022-34271-z) | ||
| - [9] [SCSA](https://github.com/bioinfo-ibms-pumc/SCSA) was originally published in [*Front Genet*](https://doi.org/10.3389/fgene.2020.00490) | ||
| - [10] [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) | ||
| - [11] [VIA](https://github.com/ShobiStassen/VIA) was originally published in [*Nature Communications*](https://www.nature.com/articles/s41467-021-25773-3) | ||
| - [12] [pyDEseq2](https://github.com/owkin/PyDESeq2) was originally published in [*biorxiv*](https://www.biorxiv.org/content/10.1101/2022.12.14.520412v1) | ||
| - [13] [NOCD](https://github.com/shchur/overlapping-community-detection) was originally avaliable in [*Deep Learning on Graphs Workshop, KDD*](https://arxiv.org/abs/1909.12201) | ||
| - [14] [SIMBA](https://github.com/pinellolab/simba) was originally published in [*Nature Methods*](https://www.nature.com/articles/s41592-023-01899-8) | ||
| - [15] [GLUE](https://github.com/gao-lab/GLUE) was originally published in [*Nature Biotechnology*](https://www.nature.com/articles/s41587-022-01284-4) | ||
| - [16] [MetaTiME](https://github.com/yi-zhang/MetaTiME) was originally published in [*Nature Communications*](https://www.nature.com/articles/s41467-023-38333-8) | ||
| - [17] [TOSICA](https://github.com/JackieHanLab/TOSICA) was originally published in [*Nature Communications*](https://doi.org/10.1038/s41467-023-35923-4) | ||
| - [18] [Harmony](https://github.com/slowkow/harmonypy/) was originally published in [*Nature Methods*](https://www.nature.com/articles/s41592-019-0619-0) | ||
| - [19] [Scanorama](https://github.com/brianhie/scanorama) was originally published in [*Nature Biotechnology*](https://www.nature.com/articles/s41587-019-0113-3) | ||
| - [20] [Combat](https://github.com/epigenelabs/pyComBat/) was originally published in [*biorxiv*](https://doi.org/10.1101/2020.03.17.995431) | ||
| - [21] [TAPE](https://github.com/poseidonchan/TAPE) was originally published in [*Nature Communications*](https://doi.org/10.1038/s41467-022-34550-9) | ||
| - [22] [SEACells](https://github.com/dpeerlab/SEACells) was originally published in [*Nature Biotechnology*](https://www.nature.com/articles/s41587-023-01716-9) | ||
| - [23] [Palantir](https://github.com/dpeerlab/Palantir) was originally published in [*Nature Biotechnology*](https://doi.org/10.1038/s41587-019-0068-49) | ||
| - [24] [STAGATE](https://github.com/QIFEIDKN/STAGATE_pyG) was originally published in [*Nature Communications*](https://www.nature.com/articles/s41467-022-29439-6) | ||
| - [25] [scVI](https://github.com/scverse/scvi-tools) was originally published in [*Nature Biotechnology*](https://doi.org/10.1038/s41587-021-01206-w) | ||
| - [26] [MIRA](https://github.com/cistrome/MIRA) was originally published in [*Nature Methods*](https://www.nature.com/articles/s41592-022-01595-z) | ||
| - [27] [Tangram](https://github.com/broadinstitute/Tangram/) was originally published in [*Nature Methods*](https://www.nature.com/articles/s41592-021-01264-7) | ||
| - [28] [STAligner](https://github.com/zhoux85/STAligner) was originally published in [*Nature Computational Science*](https://doi.org/10.1038/s43588-023-00528-w) | ||
| - [29] [CEFCON](https://github.com/WPZgithub/CEFCON) was originally published in [*Nature Communications*](https://www.nature.com/articles/s41467-023-44103-3) | ||
| - [30] [PyComplexHeatmap](https://github.com/DingWB/PyComplexHeatmap) was originally published in [*iMeta*](https://doi.org/10.1002/imt2.115) | ||
| - [31] [STT](https://github.com/cliffzhou92/STT/) was originally published in [*Nature Method*](https://www.nature.com/articles/s41592-024-02266-x#Sec2) | ||
| - [32] [SLAT](https://github.com/gao-lab/SLAT) was originally published in [*Nature Communications*](https://www.nature.com/articles/s41467-023-43105-5) | ||
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| ## Included Package not published or preprint | ||
| ## `4` [Data Framework and Reference](#) | ||
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| The omicverse is implemented as an infrastructure based on the following four data structures. | ||
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| <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> | ||
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| </table> | ||
| </div> | ||
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| --- | ||
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| The table contains the tools have been published | ||
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| <div align="center"> | ||
| <table> | ||
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| <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> | ||
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| <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">VIA<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> | ||
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| <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> | ||
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| <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> | ||
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| <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> | ||
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| <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> | ||
| </tr> | ||
| </table> | ||
| </div> | ||
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| --- | ||
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| **Included Package not published or preprint** | ||
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| - [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. | ||
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| ## Contact | ||
| ## `5` [Contact](#) | ||
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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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| ## Developer Guild | ||
| ## `6` [Developer Guild and Acknowledgements](#) | ||
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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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| ## Acknowledgements | ||
| > [!IMPORTANT] | ||
| > We would like to thank the following WeChat Official Accounts for promoting Omicverse. | ||
| We would like to thank the following WeChat Official Accounts for promoting Omicverse. | ||
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| <p align="left"> <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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| ## Other | ||
| <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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| If you would like to sponsor the development of our project, you can go to the afdian website (https://afdian.net/a/starlitnightly) and sponsor us. | ||
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| <div>Logo made by <a href="https://www.designevo.com/" title="Free Online Logo Maker">DesignEvo free logo creator</a></div> | ||
| > [!TIP] | ||
| > <div>Logo made by <a href="https://www.designevo.com/" title="Free Online Logo Maker">DesignEvo free logo creator</a></div> | ||
| Copyright © 2024 [112 Lab](). <br /> | ||
| This project is [GPL3.0](./LICENSE) licensed. | ||
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| <!-- LINK GROUP --> | ||
| [docs-feat-provider]: https://starlitnightly.github.io/omicverse/ | ||