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

rancovr: Cluster detection in R with RAndom Neighbourhood COVeRing

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.

metagenomics pipeline supporting The UnO Project for identifying pathogens in common across outbreak samples

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.

In this repo. , "Cost Effective Lazy Forward Selection" Algorithm is implemented from scratch in python with only numpy library.

In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.

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.

Implementation of Complex Networks Algorithms