OmicVerse: A single pipeline for exploring the entire transcriptome universe
Project description
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
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Star History
1 Introduction
The original name of the omicverse was 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.
2 Directory structure
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โโโ omicverse # Main Python package
โโโ omicverse_guide # Documentation files
โโโ sample # Some test data
โโโ LICENSE
โโโ 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 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 or omicverse.readthedocs.io.
4 Data Framework and Reference
The omicverse is implemented as an infrastructure based on the following four data structures.
The table contains the tools have been published
| Scanpy ๐ฆ ๐ |
dynamicTreeCut ๐ฆ ๐ |
scDrug ๐ฆ ๐ |
MOFA ๐ฆ ๐ |
COSG ๐ฆ ๐ |
CellphoneDB ๐ฆ ๐ |
| AUCell ๐ฆ ๐ |
Bulk2Space ๐ฆ ๐ |
SCSA ๐ฆ ๐ |
WGCNA ๐ฆ ๐ |
VIA ๐ฆ ๐ |
pyDEseq2 ๐ฆ ๐ |
| NOCD ๐ฆ ๐ |
SIMBA ๐ฆ ๐ |
GLUE ๐ฆ ๐ |
MetaTiME ๐ฆ ๐ |
TOSICA ๐ฆ ๐ |
Harmony ๐ฆ ๐ |
| Scanorama ๐ฆ ๐ |
Combat ๐ฆ ๐ |
TAPE ๐ฆ ๐ |
SEACells ๐ฆ ๐ |
Palantir ๐ฆ ๐ |
STAGATE ๐ฆ ๐ |
| scVI ๐ฆ ๐ |
MIRA ๐ฆ ๐ |
Tangram ๐ฆ ๐ |
STAligner ๐ฆ ๐ |
CEFCON ๐ฆ ๐ |
PyComplexHeatmap ๐ฆ ๐ |
| STT ๐ฆ ๐ |
SLAT ๐ฆ ๐ |
GPTCelltype ๐ฆ ๐ |
PROST ๐ฆ ๐ |
CytoTrace2 ๐ฆ ๐ |
GraphST ๐ฆ ๐ |
| COMPOSITE ๐ฆ ๐ |
mellon ๐ฆ ๐ |
starfysh ๐ฆ ๐ |
Included Package not published or preprint
- [1] Cellula is to provide a toolkit for the exploration of scRNA-seq. These tools perform common single-cell analysis tasks
- [2] 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 is an analysis pipeline for inferring gene expression programs from single-cell RNA-Seq (scRNA-Seq) data.
5 Contact
- Zehua Zeng (starlitnightly@gmail.com or zehuazeng@xs.ustb.edu.cn)
- Lei Hu (hulei@westlake.edu.cn)
6 Developer Guild and Contributing
If you would like to contribute to omicverse, please refer to our developer documentation.
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[!IMPORTANT]
We would like to thank the following WeChat Official Accounts for promoting Omicverse.
7 Citation
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.
8 Other
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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