R-universe - m-murphy (Maxwell Murphy)

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. Implements the model described in Murphy and Greenhouse (2024) <doi:10.1093/bioinformatics/btae619>.

Last updated

genomicsmalariamcmccppopenmp

4.81 score 8 stars 27 scripts

snp.slicer - Bayesian Nonparametric Resolution of Multi-Strain Infections

Implementation of SNP-Slice, a Bayesian nonparametric method for resolving multi-strain infections using slice sampling with stick-breaking construction. The algorithm simultaneously estimates strain haplotypes and links them to hosts from sequencing data. Supports multiple observation models including categorical, Poisson, binomial, and negative binomial distributions.

Last updated

cpp

3.70 score

moire - Multiplicity of Infection and Allele Frequency Recovery from Noisy Polyallelic Genetics Data

Last updated

cppopenmp

3.00 score

eppicenter.tools - An Amazing Shiny App

What the package does (one paragraph).

Last updated

1.00 score 1 stars