omicverse 1.4.1

OmicVerse: A single pipeline for exploring the entire transcriptome universe

OmicVerse is the fundamental package for multi omics included bulk and single cell analysis with Python.

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.

Directory structure

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

Where to get it

Binary installers for the latest released version are available at the pypi

pip install -U omicverse

Usage

Please checkout the documentations and tutorials at omicverse.readthedocs.io.

Reference

• [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

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.

Contact

• Zehua Zeng ([e-mail] or [e-mail])

Other

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