This library provides an installable implementation of the original snp-slice model. We have no affiliation with this author and provide this implementation as is.
SNP-Slice is a Bayesian nonparametric method for resolving multi-strain infections using slice sampling. The algorithm simultaneously estimates strain haplotypes and links them to hosts from SNP data.
# Install from our r-universe
install.packages(
'snp.slicer',
repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org')
)- Multiple Observation Models: Supports categorical, Poisson, binomial, and negative binomial models
- Flexible Data Input: Accepts read count data, categorical data (matrix or long-format data.frame with counts converted to 0/0.5/1), or file paths
- Convergence Diagnostics: Built-in monitoring and early stopping
- Comprehensive Results: Returns allocation matrix, dictionary matrix, and diagnostics
If you use SNP-Slice in your research, please cite:
@article{Ju_Liu_He_2024,
title={SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts},
volume={40},
ISSN={1367-4811},
DOI={10.1093/bioinformatics/btae344},
number={6},
journal={Bioinformatics},
author={Ju, Nianqiao and Liu, Jiawei and He, Qixin},
year={2024},
month=june,
pages={btae344}
}
This package is licensed under the GPL-3 License.