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.

All release notes can be found in doc/release.rst.
vireoSNP_donors.ipynb giving example on donor deconvolution manually
vireoSNP_clones.ipynb giving example clone reconstruction on mitochondral mutations
donor_match.ipynb gives example on aligning donors to other omics data or other batches

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.

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.

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

Source distribution for vireoSNP 0.4.1
File	Size	Uploaded
vireoSNP-0.4.1.tar.gz	1.6 MB	Sep 17, 2020	Details

Download URL	vireoSNP-0.4.1.tar.gz
Size	1.6 MB
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Upload date	Sep 17, 2020
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