dcifer - Genetic Relatedness Between Polyclonal Infections
An implementation of Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent (IBD) based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. The package includes functions that format and preprocess the data, implement the method, and visualize the results. Gerlovina et al. (2022) <doi:10.1093/genetics/iyac126>.
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5.85 score 8 stars 25 scripts 221 downloads
moire - Multiplicity of Infection and Allele Frequency Recovery from Noisy Polyallelic Genetics Data
A Markov Chain Monte Carlo (MCMC) based approach to Bayesian estimation of individual level multiplicity of infection, within host relatedness, and population allele frequencies from polyallelic genetic data.
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genomicsmalariamcmccppopenmp
4.24 score 7 stars 25 scripts