| Main use-cases | MOI estimation |
| Authors | Aris Paschalidis, OJ Watson |
| Latest version | 0.1.2 |
| License | MIT |
| Website | bailey-lab.github.io/coiaf |
| Code repository | https://github.com/bailey-lab/coiaf/ |
| Publication | https://doi.org/10.1371/journal.pcbi.1010247 |
| Tutorial authors | Maxwell Murphy |
| Tutorial date | 11-Dec-2023 |
coiaf
Summary sheet
Purpose
coiaf is a package for estimating complexity of infection (COI) from bi-allelic SNP data. In comparison to other available methods, coiaf is fast, accurate, and can be used to estimate COI for a large number of samples.
Existing resources
The coiaf website contains a detailed tutorial on how to use the package, as well as a vignette with worked examples.
The paper describing the package is available here.
Citation
@article{
Paschalidis_Watson_Aydemir_Verity_Bailey_2023,
title={coiaf: Directly estimating complexity of infection with allele frequencies},
volume={19},
ISSN={1553-7358},
DOI={10.1371/journal.pcbi.1010247},
number={6},
journal={PLOS Computational Biology},
publisher={Public Library of Science},
author={Paschalidis, Aris and Watson, Oliver J. and Aydemir, Ozkan and Verity, Robert and Bailey, Jeffrey A.},
year={2023},
month=jun,
pages={e1010247},
language={en}
}