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
The easiest way is to install via PyPI by typing this line is terminal:
pip install vireoSNP
Alternatively, you can always download this repository and install manually:
python setup.py install
For more options of installation, see the full installation.
Usage and manual
Genotyping for each cell (pre-step)
There might be some bioinformatics efforts in this step, however, a few existing software can provide a solution. There are often two steps for this:
identify candidate SNPs: known common SNPs / freebayes / cellSNP
genotype candidate SNPs in each cell: cellSNP / vartrix / bcftools mpileup
See more introduction in the genotyping section.
Demultiplexing from allelic expression
This python package offers a set of utilities functions and an executable command line vireo for donor deconvolution in any of these four situations
without any genotype:
vireo -c $CELL_DATA -N $n_donor -o $OUT_DIR
with genotype for all samples (tag via -t: GT, GP, or PL)
vireo -c $CELL_DATA -d $DONOR_GT_FILE -o $OUT_DIR
with genotype for part of the samples
vireo -c $CELL_DATA -d $DONOR_GT_FILE -o $OUT_DIR -N $n_donor
with genotype but not confident
vireo -c $CELL_DATA -d $DONOR_GT_FILE -o $OUT_DIR --forceLearnGT
The cell data can be any of the following two formats:
standard VCF file with variants by cells
a cellSNP output folder containing VCF for variants info and sparse matrices AD and DP
For details, see the full manual or type “vireo -h” for all arguments. We also provide a demo.sh for running the test data sets in this repo.
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.
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Metadata
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Release files for vireoSNP 0.1.2
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| File | Size | Uploaded | |
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Release files / vireoSNP-0.1.2.tar.gz
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