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.
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├── omicverse # Main Python package
├── omicverse_guide # Documentation files
├── sample # Some test data
├── LICENSE
└── README.mdBinary installers for the latest released version are available at the pypi
pip install -U omicversePlease checkout the documentations and tutorials at omicverse.readthedocs.io.
- [1] dynamicTreeCut was originally published by in Bioinformatics
- [2] scDrug was originally published in Computational and Structural Biotechnology Journal
- [3] MOFA was originally published in Genome Biology
- [4] COSG was originally published in Briefings in Bioinformatics
- [5] CellphoneDB was originally published in Nature
- [6] AUCell was originally available in Bioconductor, and we use the script of Pyscenic to instead.
- [7] Bulk2Space was originally available in Nature Communications
- [8] SCSA was originally availabale in Front Genet
- [9] WGCNA was originally avaliable in BMC Bioinformatics
- [10] VIA was originally avaliable in Nature Communications
- [11] pyDEseq2 was originally avaliable in biorxiv
- [12] NOCD was originally avaliable in Deep Learning on Graphs Workshop, KDD
- [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.
- Zehua Zeng (starlitnightly@163.com or zehuazeng@xs.ustb.edu.cn)
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