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OmicVerse: A single pipeline for exploring the entire transcriptome universe

Project description

pypi-badge Documentation Status pypiDownloads condaDownloads License:GPL scverse Pytest

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

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.

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.

omicverse-light omicverse-dark

Directory structure

├── omicverse                  # Main Python package
├── omicverse_guide            # Documentation files
├── sample                     # Some test data

Where to get it

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

Data Framework


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.


Developer Guild

If you would like to contribute to omicverse, please refer to our developer documentation.


We would like to thank the following WeChat Official Accounts for promoting Omicverse.

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Project details

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