BSR-Based Allele Calling Algorithm
Epidemiological surveillance in Python
cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
A Disease Outbreak Assistance system using machine learning and Artifitial Intelligence
In this repo. , "Cost Effective Lazy Forward Selection" Algorithm is implemented from scratch in python with only numpy library.
metagenomics pipeline supporting The UnO Project for identifying pathogens in common across outbreak samples
In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.
R scripts used in M Cavallaro, L Dyson, MJ Tildesly, D Todkill & MJ Keeling (2023) Spatio-temporal surveillance and early detection of SARS-CoV-2 variants of concern. J. R. Soc. Interface. 20: 20230410. 20230410.
Implementation of Complex Networks Algorithms
rancovr: Cluster detection in R with RAndom Neighbourhood COVeRing
Software supporting M. Cavallaro, et al., Cluster detection with random neighbourhood covering: Application to invasive Group A Streptococcal disease. PLoS Comput Biol 18(11): e1010726 (2022) https://doi.org/10.1371/journal.pcbi.1010726.
A machine learning project focused on predicting genetic shifts in future Ebola outbreaks using genomic data. The project analyzes historical Ebola sequences to forecast potential mutations and viral characteristics, aiding in outbreak preparedness and public health responses.
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