vireoSNP

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

All release notes can be found in doc/release.rst.
vireoSNP_usage.ipynb for using vireoSNP on donor deconvolution and general cell clustering by modelling allelic ratios

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 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)

Metadata

Release files for vireoSNP 0.2.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for vireoSNP 0.2.2
File	Size	Uploaded
vireoSNP-0.2.2.tar.gz	20.5 kB	Mar 22, 2020	Details

Release files / vireoSNP-0.2.2.tar.gz

Download URL	vireoSNP-0.2.2.tar.gz
Size	20.5 kB
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SHA-256 checksum How to use checksums	`e6613cd09b9aed5f860c917172f97c6e29e23b9d5297cdec0b630ac3aac93d92`
BLAKE2b-256 checksum How to use checksums	`9a5c46115fe88a5a5399c059666dd0e188c5302417b803c43ea570e21e27842b`
Upload date	Mar 22, 2020
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/3.1.1 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.4.0 requests-toolbelt/0.9.1 tqdm/4.36.1 CPython/3.7.4`