metagenomics pipeline supporting The UnO Project for identifying pathogens in common across outbreak samples
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Updated
May 10, 2024 - Nextflow
metagenomics pipeline supporting The UnO Project for identifying pathogens in common across outbreak samples
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.
rancovr: Cluster detection in R with RAndom Neighbourhood COVeRing
In this repo. , "Cost Effective Lazy Forward Selection" Algorithm is implemented from scratch in python with only numpy library.
risk modelling for virbrio infections and estimating the attributable rates
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.
Implementation of Complex Networks Algorithms
A Disease Outbreak Assistance system using machine learning and Artifitial Intelligence
cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
Epidemiological surveillance in Python
BSR-Based Allele Calling Algorithm
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