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code monkey
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code monkey
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ciarajudge/README.md

Hey, my name is Ciara 👋

I'm a PhD student at the London School of Hygiene and Tropical Medicine, and I work on methods for modelling infectious disease outbreaks that incorporate traditional epidemiology as well as genetic data.

I love software development, maths, biology and science communication, and I try to use my passion for all of these things to make a positive difference in the field of human health. I'm currently working on EpiFusion, a program for jointly inferring outbreak trajectories and transmission dynamics by integrating phylodynamics and epidemiology via particle filtering.

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  1. EpiFusion EpiFusion Public

    Repository for EpiFusion, an infectious disease modelling framework built on the principles of phylodynamics and epidemiology

    Java 10 1

  2. EpiFusionUtilities EpiFusionUtilities Public

    R package for parsing output from EpiFusion joint phylodynamic and epidemiological inference software

    R

  3. EvoCov EvoCov Public

    This is EvoCov, a pipeline designed for analysis of SARS-CoV-2 sequences from GISAID.

    Python 6

  4. OncoSim OncoSim Public

    SNV and CNA profile simulation of a tumour with multiple subclones. Capability also for metastasis simulation.

    R

  5. SCAMP_Proteomics SCAMP_Proteomics Public

    Automated pipeline for proteomic analysis of PRIDE raw files using maxquant

    Python 2

  6. EpiFusion_PublicationRepo EpiFusion_PublicationRepo Public

    Repository to fully reproduce the results of the manuscript 'EpiFusion: joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle …

    R