Skip to main content

vireoSNP - donor deconvolution for multiplexed scRNA-seq data

Project description

PyPI Docs Build Status

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.

Installation

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

pip install vireoSNP

Alternatively, you can download or clone this repository and type python setup.py install to install. In either case, add --user if you don’t have the permission as a root or 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 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. bioRxiv (2019): 598748.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

vireoSNP-0.1.7.tar.gz (17.3 kB view details)

Uploaded Source

File details

Details for the file vireoSNP-0.1.7.tar.gz.

File metadata

  • Download URL: vireoSNP-0.1.7.tar.gz
  • Upload date:
  • Size: 17.3 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.12.1 pkginfo/1.4.2 requests/2.18.4 setuptools/39.1.0 requests-toolbelt/0.8.0 tqdm/4.28.1 CPython/3.6.8

File hashes

Hashes for vireoSNP-0.1.7.tar.gz
Algorithm Hash digest
SHA256 65b284b5c13c96a723a73576d2659f4ca1f2b3fcae88e329865f57ccf957e47b
MD5 48fe8830efa257541e3c774f5ae0e354
BLAKE2b-256 e5466bf6ec7e39f14e7ed35e87d942b6f25c5fa768822f750bdd02f642bde5bb

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page