Skip to content

Demultiplexing pooled scRNA-seq data without genotype reference

License

Notifications You must be signed in to change notification settings

houruiyan/vireo

 
 

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

61 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

PyPI Docs Build Status DOI

vireo: donor deconvolution for pooled single-cell data

Vireo: Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in multiplexed scRNA-seq data.

The name vireo follows the theme from cardelino (for clone deconvolution), while the Python package name is vireoSNP to aviod name confilict on PyPI.

News

Installation

Vireo is available through PyPI. To install, type the following command line, and add -U for upgrading:

pip install -U vireoSNP

Alternatively, you can install from this GitHub repository for latest (often development) version by following command line

pip install -U git+https://github.com/single-cell-genetics/vireo

In either case, add --user if you don't have the write permission for your Python environment.

For more instructions, see the installation manual.

Manual and examples

The full manual is at https://vireoSNP.readthedocs.io It includes more details on installation, demultiplex usage, and preprocess with genotyping cells.

Test example data is included in this repo and demos can be found in examples/demo.sh.

Also, type vireo -h for all arguments with the version you are using.

Reference

Yuanhua Huang, Davis J. McCarthy, and Oliver Stegle. Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference. Genome Biology 20, 273 (2019)

About

Demultiplexing pooled scRNA-seq data without genotype reference

Resources

License

Stars

Watchers

Forks

Packages

No packages published

Languages

  • Python 100.0%